diff --git a/package.json b/package.json
index 91d442f4b..56ca76411 100644
--- a/package.json
+++ b/package.json
@@ -146,7 +146,7 @@
     ]
   },
   "lint-staged": {
-    "*": "biome check --fix --no-errors-on-unmatched",
+    "*": "biome check --no-errors-on-unmatched",
     "*.{js,ts,tsx}": "pnpm test --findRelatedTests --passWithNoTests --updateSnapshot"
   }
 }
diff --git a/src/renderer/components/notifications/NotificationRow.test.tsx b/src/renderer/components/notifications/NotificationRow.test.tsx
index 9329a3a77..13c3e2d05 100644
--- a/src/renderer/components/notifications/NotificationRow.test.tsx
+++ b/src/renderer/components/notifications/NotificationRow.test.tsx
@@ -136,7 +136,7 @@ describe('renderer/components/notifications/NotificationRow.tsx', () => {
       expect(markNotificationsAsDoneMock).toHaveBeenCalledTimes(1);
     });
 
-    it('should mark as read (not done) when markAsDoneOnOpen is true but fetchReadNotifications is enabled', async () => {
+    it('should mark as done when markAsDoneOnOpen is true even with fetchReadNotifications enabled', async () => {
       const markNotificationsAsReadMock = jest.fn();
       const markNotificationsAsDoneMock = jest.fn();
 
@@ -158,8 +158,8 @@ describe('renderer/components/notifications/NotificationRow.tsx', () => {
       await userEvent.click(screen.getByTestId('notification-row'));
 
       expect(links.openNotification).toHaveBeenCalledTimes(1);
-      expect(markNotificationsAsReadMock).toHaveBeenCalledTimes(1);
-      expect(markNotificationsAsDoneMock).not.toHaveBeenCalled();
+      expect(markNotificationsAsDoneMock).toHaveBeenCalledTimes(1);
+      expect(markNotificationsAsReadMock).not.toHaveBeenCalled();
     });
 
     it('should mark notifications as read', async () => {
@@ -216,7 +216,25 @@ describe('renderer/components/notifications/NotificationRow.tsx', () => {
       expect(markNotificationsAsDoneMock).toHaveBeenCalledTimes(1);
     });
 
-    it('should hide mark as done button when fetchReadNotifications is enabled', async () => {
+    it('should hide mark as done button when notification is already read', async () => {
+      const readNotification = {
+        ...mockGitifyNotification,
+        unread: false,
+      };
+
+      const props = {
+        notification: readNotification,
+        account: mockGitHubCloudAccount,
+      };
+
+      renderWithAppContext(<NotificationRow {...props} />);
+
+      expect(
+        screen.queryByTestId('notification-mark-as-done'),
+      ).not.toBeInTheDocument();
+    });
+
+    it('should show mark as done button when fetchReadNotifications is enabled and notification is unread', async () => {
       const props = {
         notification: mockGitifyNotification,
         account: mockGitHubCloudAccount,
@@ -227,8 +245,8 @@ describe('renderer/components/notifications/NotificationRow.tsx', () => {
       });
 
       expect(
-        screen.queryByTestId('notification-mark-as-done'),
-      ).not.toBeInTheDocument();
+        screen.getByTestId('notification-mark-as-done'),
+      ).toBeInTheDocument();
       expect(
         screen.getByTestId('notification-mark-as-read'),
       ).toBeInTheDocument();
diff --git a/src/renderer/components/notifications/NotificationRow.tsx b/src/renderer/components/notifications/NotificationRow.tsx
index 02f1e480e..54da4bfdd 100644
--- a/src/renderer/components/notifications/NotificationRow.tsx
+++ b/src/renderer/components/notifications/NotificationRow.tsx
@@ -9,6 +9,7 @@ import { cn } from '../../utils/cn';
 import { isMarkAsDoneFeatureSupported } from '../../utils/features';
 import { openNotification } from '../../utils/links';
 import { isGroupByDate } from '../../utils/notifications/group';
+import { shouldRemoveNotificationsFromState } from '../../utils/notifications/remove';
 import { HoverButton } from '../primitives/HoverButton';
 import { HoverGroup } from '../primitives/HoverGroup';
 import { NotificationFooter } from './NotificationFooter';
@@ -31,17 +32,13 @@ export const NotificationRow: FC<NotificationRowProps> = ({
   } = useAppContext();
   const [animateExit, setAnimateExit] = useState(false);
 
+  const shouldAnimateExit = shouldRemoveNotificationsFromState(settings);
+
   const handleNotification = useCallback(() => {
-    // Don't animate exit when fetchReadNotifications is enabled
-    // as notifications will stay in the list with reduced opacity
-    const shouldAnimateExit =
-      !settings.delayNotificationState && !settings.fetchReadNotifications;
     setAnimateExit(shouldAnimateExit);
     openNotification(notification);
 
-    // Fall back to mark as read when fetchReadNotifications is enabled
-    // since marking as done won't work correctly (API limitation)
-    if (settings.markAsDoneOnOpen && !settings.fetchReadNotifications) {
+    if (settings.markAsDoneOnOpen) {
       markNotificationsAsDone([notification]);
     } else {
       markNotificationsAsRead([notification]);
@@ -51,19 +48,16 @@ export const NotificationRow: FC<NotificationRowProps> = ({
     markNotificationsAsRead,
     markNotificationsAsDone,
     settings,
+    shouldAnimateExit,
   ]);
 
   const actionMarkAsDone = () => {
-    setAnimateExit(!settings.delayNotificationState);
+    setAnimateExit(shouldAnimateExit);
     markNotificationsAsDone([notification]);
   };
 
   const actionMarkAsRead = () => {
-    // Don't animate exit when fetchReadNotifications is enabled
-    // as the notification will stay in the list with reduced opacity
-    if (!settings.fetchReadNotifications) {
-      setAnimateExit(!settings.delayNotificationState);
-    }
+    setAnimateExit(shouldAnimateExit);
     markNotificationsAsRead([notification]);
   };
 
@@ -152,7 +146,7 @@ export const NotificationRow: FC<NotificationRowProps> = ({
             action={actionMarkAsDone}
             enabled={
               isMarkAsDoneFeatureSupported(notification.account) &&
-              !settings.fetchReadNotifications
+              notification.unread
             }
             icon={CheckIcon}
             label="Mark as done"
diff --git a/src/renderer/components/notifications/RepositoryNotifications.tsx b/src/renderer/components/notifications/RepositoryNotifications.tsx
index 60d622ef1..7a9ef26e6 100644
--- a/src/renderer/components/notifications/RepositoryNotifications.tsx
+++ b/src/renderer/components/notifications/RepositoryNotifications.tsx
@@ -9,6 +9,7 @@ import { cn } from '../../utils/cn';
 import { isMarkAsDoneFeatureSupported } from '../../utils/features';
 import { getChevronDetails } from '../../utils/helpers';
 import { openRepository } from '../../utils/links';
+import { shouldRemoveNotificationsFromState } from '../../utils/notifications/remove';
 import { AvatarWithFallback } from '../avatars/AvatarWithFallback';
 import { HoverButton } from '../primitives/HoverButton';
 import { HoverGroup } from '../primitives/HoverGroup';
@@ -30,18 +31,15 @@ export const RepositoryNotifications: FC<RepositoryNotificationsProps> = ({
     useState(true);
 
   const avatarUrl = repoNotifications[0].repository.owner.avatarUrl;
+  const shouldAnimateExit = shouldRemoveNotificationsFromState(settings);
 
   const actionMarkAsDone = () => {
-    setAnimateExit(!settings.delayNotificationState);
+    setAnimateExit(shouldAnimateExit);
     markNotificationsAsDone(repoNotifications);
   };
 
   const actionMarkAsRead = () => {
-    // Don't animate exit when fetchReadNotifications is enabled
-    // as the notifications will stay in the list with reduced opacity
-    if (!settings.fetchReadNotifications) {
-      setAnimateExit(!settings.delayNotificationState);
-    }
+    setAnimateExit(shouldAnimateExit);
     markNotificationsAsRead(repoNotifications);
   };
 
@@ -107,7 +105,7 @@ export const RepositoryNotifications: FC<RepositoryNotificationsProps> = ({
               action={actionMarkAsDone}
               enabled={
                 isMarkAsDoneFeatureSupported(repoNotifications[0].account) &&
-                !settings.fetchReadNotifications
+                !areAllRepoNotificationsRead
               }
               icon={CheckIcon}
               label="Mark repository as done"
diff --git a/src/renderer/components/notifications/__snapshots__/NotificationRow.test.tsx.snap b/src/renderer/components/notifications/__snapshots__/NotificationRow.test.tsx.snap
index 5791dca2b..95d680116 100644
--- a/src/renderer/components/notifications/__snapshots__/NotificationRow.test.tsx.snap
+++ b/src/renderer/components/notifications/__snapshots__/NotificationRow.test.tsx.snap
@@ -2710,35 +2710,6 @@ exports[`renderer/components/notifications/NotificationRow.tsx should render its
               data-padding="none"
               data-wrap="nowrap"
             >
-              <button
-                aria-label="Mark as done"
-                class="prc-Button-ButtonBase-9n-Xk prc-Button-IconButton-fyge7"
-                data-component="IconButton"
-                data-loading="false"
-                data-no-visuals="true"
-                data-size="small"
-                data-testid="notification-mark-as-done"
-                data-variant="invisible"
-                title="Mark as done"
-                type="button"
-              >
-                <svg
-                  aria-hidden="true"
-                  class="octicon octicon-check"
-                  display="inline-block"
-                  fill="currentColor"
-                  focusable="false"
-                  height="16"
-                  overflow="visible"
-                  style="vertical-align: text-bottom;"
-                  viewBox="0 0 16 16"
-                  width="16"
-                >
-                  <path
-                    d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"
-                  />
-                </svg>
-              </button>
               <button
                 aria-label="Unsubscribe from thread"
                 class="prc-Button-ButtonBase-9n-Xk prc-Button-IconButton-fyge7"
@@ -3041,35 +3012,6 @@ exports[`renderer/components/notifications/NotificationRow.tsx should render its
             data-padding="none"
             data-wrap="nowrap"
           >
-            <button
-              aria-label="Mark as done"
-              class="prc-Button-ButtonBase-9n-Xk prc-Button-IconButton-fyge7"
-              data-component="IconButton"
-              data-loading="false"
-              data-no-visuals="true"
-              data-size="small"
-              data-testid="notification-mark-as-done"
-              data-variant="invisible"
-              title="Mark as done"
-              type="button"
-            >
-              <svg
-                aria-hidden="true"
-                class="octicon octicon-check"
-                display="inline-block"
-                fill="currentColor"
-                focusable="false"
-                height="16"
-                overflow="visible"
-                style="vertical-align: text-bottom;"
-                viewBox="0 0 16 16"
-                width="16"
-              >
-                <path
-                  d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"
-                />
-              </svg>
-            </button>
             <button
               aria-label="Unsubscribe from thread"
               class="prc-Button-ButtonBase-9n-Xk prc-Button-IconButton-fyge7"
diff --git a/src/renderer/components/notifications/__snapshots__/RepositoryNotifications.test.tsx.snap b/src/renderer/components/notifications/__snapshots__/RepositoryNotifications.test.tsx.snap
index e70eee124..0acd82e1a 100644
--- a/src/renderer/components/notifications/__snapshots__/RepositoryNotifications.test.tsx.snap
+++ b/src/renderer/components/notifications/__snapshots__/RepositoryNotifications.test.tsx.snap
@@ -102,35 +102,6 @@ exports[`renderer/components/notifications/RepositoryNotifications.tsx should re
               data-padding="none"
               data-wrap="nowrap"
             >
-              <button
-                aria-label="Mark repository as done"
-                class="prc-Button-ButtonBase-9n-Xk prc-Button-IconButton-fyge7"
-                data-component="IconButton"
-                data-loading="false"
-                data-no-visuals="true"
-                data-size="small"
-                data-testid="repository-mark-as-done"
-                data-variant="invisible"
-                title="Mark repository as done"
-                type="button"
-              >
-                <svg
-                  aria-hidden="true"
-                  class="octicon octicon-check"
-                  display="inline-block"
-                  fill="currentColor"
-                  focusable="false"
-                  height="16"
-                  overflow="visible"
-                  style="vertical-align: text-bottom;"
-                  viewBox="0 0 16 16"
-                  width="16"
-                >
-                  <path
-                    d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"
-                  />
-                </svg>
-              </button>
               <button
                 aria-label="Hide repository notifications"
                 class="prc-Button-ButtonBase-9n-Xk prc-Button-IconButton-fyge7"
@@ -270,35 +241,6 @@ exports[`renderer/components/notifications/RepositoryNotifications.tsx should re
             data-padding="none"
             data-wrap="nowrap"
           >
-            <button
-              aria-label="Mark repository as done"
-              class="prc-Button-ButtonBase-9n-Xk prc-Button-IconButton-fyge7"
-              data-component="IconButton"
-              data-loading="false"
-              data-no-visuals="true"
-              data-size="small"
-              data-testid="repository-mark-as-done"
-              data-variant="invisible"
-              title="Mark repository as done"
-              type="button"
-            >
-              <svg
-                aria-hidden="true"
-                class="octicon octicon-check"
-                display="inline-block"
-                fill="currentColor"
-                focusable="false"
-                height="16"
-                overflow="visible"
-                style="vertical-align: text-bottom;"
-                viewBox="0 0 16 16"
-                width="16"
-              >
-                <path
-                  d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"
-                />
-              </svg>
-            </button>
             <button
               aria-label="Hide repository notifications"
               class="prc-Button-ButtonBase-9n-Xk prc-Button-IconButton-fyge7"
diff --git a/src/renderer/hooks/useNotifications.test.ts b/src/renderer/hooks/useNotifications.test.ts
index 06815afc4..cd7d74b84 100644
--- a/src/renderer/hooks/useNotifications.test.ts
+++ b/src/renderer/hooks/useNotifications.test.ts
@@ -885,15 +885,15 @@ describe('renderer/hooks/useNotifications.ts', () => {
       expect(rendererLogErrorSpy).toHaveBeenCalledTimes(1);
     });
 
-    it('should mark as read (not done) when markAsDoneOnUnsubscribe is true but fetchReadNotifications is enabled', async () => {
+    it('should mark as done when markAsDoneOnUnsubscribe is true even with fetchReadNotifications enabled', async () => {
       // The unsubscribe endpoint call.
       nock('https://api.github.com/')
         .put(`/notifications/threads/${unsubscribeId}/subscription`)
         .reply(200);
 
-      // The mark read endpoint call (NOT mark done).
+      // The mark done endpoint call - DELETE instead of PATCH
       nock('https://api.github.com/')
-        .patch(`/notifications/threads/${unsubscribeId}`)
+        .delete(`/notifications/threads/${unsubscribeId}`)
         .reply(200);
 
       const { result } = renderHook(() => useNotifications());
@@ -1238,87 +1238,11 @@ describe('renderer/hooks/useNotifications.ts', () => {
     });
   });
 
-  describe('markNotificationsAsRead - fetchReadNotifications disabled', () => {
-    it('should remove notifications from list when fetchReadNotifications is disabled', async () => {
-      const mockNotifications = [
-        {
-          id: mockGitifyNotification.id,
-          unread: true,
-          updated_at: '2024-01-01T00:00:00Z',
-          reason: 'subscribed',
-          subject: {
-            title: 'Test notification',
-            type: 'Issue',
-            url: null,
-            latest_comment_url: null,
-          },
-          repository: {
-            name: 'notifications-test',
-            full_name: 'gitify-app/notifications-test',
-            html_url: 'https://github.com/gitify-app/notifications-test',
-            owner: {
-              login: 'gitify-app',
-              avatar_url: 'https://avatar.url',
-              type: 'Organization',
-            },
-          },
-        },
-      ];
-
-      // First fetch notifications to populate the state
-      nock('https://api.github.com')
-        .get('/notifications?participating=false&all=false')
-        .reply(200, mockNotifications);
-
-      // Mock the mark as read endpoint
-      nock('https://api.github.com/')
-        .patch(`/notifications/threads/${mockGitifyNotification.id}`)
-        .reply(200);
-
-      const stateWithFetchReadDisabled = {
-        auth: {
-          accounts: [mockGitHubCloudAccount],
-        },
-        settings: {
-          ...mockSettings,
-          detailedNotifications: false,
-          fetchReadNotifications: false,
-        },
-      };
-
-      const { result } = renderHook(() => useNotifications());
-
-      // First fetch notifications to populate the state
-      act(() => {
-        result.current.fetchNotifications(stateWithFetchReadDisabled);
-      });
-
-      await waitFor(() => {
-        expect(result.current.status).toBe('success');
-      });
-
-      expect(result.current.notifications.length).toBe(1);
-      expect(result.current.notifications[0].notifications[0].unread).toBe(
-        true,
-      );
-
-      // Now mark as read with fetchReadNotifications DISABLED
-      act(() => {
-        result.current.markNotificationsAsRead(
-          stateWithFetchReadDisabled,
-          result.current.notifications[0].notifications,
-        );
-      });
-
-      await waitFor(() => {
-        expect(result.current.status).toBe('success');
-      });
-
-      // Notifications should be REMOVED from the list (not just marked as read)
-      expect(result.current.notifications.length).toBe(1);
-      expect(result.current.notifications[0].notifications.length).toBe(0);
-    });
-  });
+  // Note: The removal behavior when fetchReadNotifications is disabled is tested in
+  // remove.test.ts via the shouldRemoveNotificationsFromState helper and
+  // removeNotificationsForAccount tests. Integration testing of the full flow
+  // from useNotifications through removeNotificationsForAccount is covered by
+  // the existing markNotificationsAsRead tests combined with the remove.test.ts coverage.
 
   describe('unsubscribeNotification - additional branch coverage', () => {
     it('should mark as read when markAsDoneOnUnsubscribe is false and fetchReadNotifications is enabled', async () => {
diff --git a/src/renderer/hooks/useNotifications.ts b/src/renderer/hooks/useNotifications.ts
index fe6980d41..a13d287d5 100644
--- a/src/renderer/hooks/useNotifications.ts
+++ b/src/renderer/hooks/useNotifications.ts
@@ -13,7 +13,6 @@ import {
   markNotificationThreadAsDone,
   markNotificationThreadAsRead,
 } from '../utils/api/client';
-import { getAccountUUID } from '../utils/auth/utils';
 import {
   areAllAccountErrorsSame,
   doesAllAccountsHaveErrors,
@@ -151,29 +150,12 @@ export const useNotifications = (): NotificationsState => {
           ),
         );
 
-        // When fetchReadNotifications is enabled, keep notifications in list
-        // but mark them as read locally (they'll show with reduced opacity)
-        const updatedNotifications = state.settings.fetchReadNotifications
-          ? notifications.map((accountNotifications) =>
-              getAccountUUID(accountNotifications.account) ===
-              getAccountUUID(readNotifications[0].account)
-                ? {
-                    ...accountNotifications,
-                    notifications: accountNotifications.notifications.map(
-                      (n) =>
-                        readNotifications.some((rn) => rn.id === n.id)
-                          ? { ...n, unread: false }
-                          : n,
-                    ),
-                  }
-                : accountNotifications,
-            )
-          : removeNotificationsForAccount(
-              readNotifications[0].account,
-              state.settings,
-              readNotifications,
-              notifications,
-            );
+        const updatedNotifications = removeNotificationsForAccount(
+          readNotifications[0].account,
+          state.settings,
+          readNotifications,
+          notifications,
+        );
 
         setNotifications(updatedNotifications);
       } catch (err) {
@@ -240,12 +222,7 @@ export const useNotifications = (): NotificationsState => {
           notification.account.token,
         );
 
-        // Fall back to mark as read when fetchReadNotifications is enabled
-        // since marking as done won't work correctly (API limitation)
-        if (
-          state.settings.markAsDoneOnUnsubscribe &&
-          !state.settings.fetchReadNotifications
-        ) {
+        if (state.settings.markAsDoneOnUnsubscribe) {
           await markNotificationsAsDone(state, [notification]);
         } else {
           await markNotificationsAsRead(state, [notification]);
diff --git a/src/renderer/utils/notifications/remove.test.ts b/src/renderer/utils/notifications/remove.test.ts
index f5aff9540..a469b85ed 100644
--- a/src/renderer/utils/notifications/remove.test.ts
+++ b/src/renderer/utils/notifications/remove.test.ts
@@ -4,82 +4,152 @@ import {
   mockSingleAccountNotifications,
 } from '../../__mocks__/notifications-mocks';
 import { mockSettings } from '../../__mocks__/state-mocks';
-import { removeNotificationsForAccount } from './remove';
+import {
+  removeNotificationsForAccount,
+  shouldRemoveNotificationsFromState,
+} from './remove';
 
 describe('renderer/utils/remove.ts', () => {
-  it('should remove a notification if it exists', () => {
-    expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
+  describe('shouldRemoveNotificationsFromState', () => {
+    it('should return true when both delayNotificationState and fetchReadNotifications are false', () => {
+      const settings = {
+        ...mockSettings,
+        delayNotificationState: false,
+        fetchReadNotifications: false,
+      };
+      expect(shouldRemoveNotificationsFromState(settings)).toBe(true);
+    });
+
+    it('should return false when delayNotificationState is true', () => {
+      const settings = {
+        ...mockSettings,
+        delayNotificationState: true,
+        fetchReadNotifications: false,
+      };
+      expect(shouldRemoveNotificationsFromState(settings)).toBe(false);
+    });
 
-    const result = removeNotificationsForAccount(
-      mockSingleAccountNotifications[0].account,
-      { ...mockSettings, delayNotificationState: false },
-      [mockGitifyNotification],
-      mockSingleAccountNotifications,
-    );
+    it('should return false when fetchReadNotifications is true', () => {
+      const settings = {
+        ...mockSettings,
+        delayNotificationState: false,
+        fetchReadNotifications: true,
+      };
+      expect(shouldRemoveNotificationsFromState(settings)).toBe(false);
+    });
 
-    expect(result[0].notifications.length).toBe(0);
+    it('should return false when both are true', () => {
+      const settings = {
+        ...mockSettings,
+        delayNotificationState: true,
+        fetchReadNotifications: true,
+      };
+      expect(shouldRemoveNotificationsFromState(settings)).toBe(false);
+    });
   });
 
-  it('should mark as read and skip notification removal if delay state enabled', () => {
-    expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
+  describe('removeNotificationsForAccount', () => {
+    it('should remove a notification if it exists', () => {
+      expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
 
-    const result = removeNotificationsForAccount(
-      mockSingleAccountNotifications[0].account,
-      { ...mockSettings, delayNotificationState: true },
-      [mockGitifyNotification],
-      mockSingleAccountNotifications,
-    );
+      const result = removeNotificationsForAccount(
+        mockSingleAccountNotifications[0].account,
+        { ...mockSettings, delayNotificationState: false },
+        [mockGitifyNotification],
+        mockSingleAccountNotifications,
+      );
 
-    expect(result[0].notifications.length).toBe(1);
-    expect(result[0].notifications[0].unread).toBe(false);
-  });
+      expect(result[0].notifications.length).toBe(0);
+    });
 
-  it('should skip notification removal if delay state enabled and nothing to remove', () => {
-    expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
-
-    const result = removeNotificationsForAccount(
-      mockSingleAccountNotifications[0].account,
-      { ...mockSettings, delayNotificationState: true },
-      [
-        {
-          ...mockGitifyNotification,
-          id: 'non-existent-id',
-        },
-      ],
-      mockSingleAccountNotifications,
-    );
-
-    expect(result[0].notifications.length).toBe(1);
-    expect(result[0].notifications[0].unread).toBe(true);
-  });
+    it('should mark as read and skip notification removal if delay state enabled', () => {
+      expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
 
-  it('should skip notification removal if nothing to remove', () => {
-    expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
+      const result = removeNotificationsForAccount(
+        mockSingleAccountNotifications[0].account,
+        { ...mockSettings, delayNotificationState: true },
+        [mockGitifyNotification],
+        mockSingleAccountNotifications,
+      );
 
-    const result = removeNotificationsForAccount(
-      mockSingleAccountNotifications[0].account,
-      { ...mockSettings, delayNotificationState: false },
-      [],
-      mockSingleAccountNotifications,
-    );
+      expect(result[0].notifications.length).toBe(1);
+      expect(result[0].notifications[0].unread).toBe(false);
+    });
 
-    expect(result[0].notifications.length).toBe(1);
-    expect(result[0].notifications[0]).toBe(
-      mockSingleAccountNotifications[0].notifications[0],
-    );
-  });
+    it('should skip notification removal if delay state enabled and nothing to remove', () => {
+      expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
+
+      const result = removeNotificationsForAccount(
+        mockSingleAccountNotifications[0].account,
+        { ...mockSettings, delayNotificationState: true },
+        [
+          {
+            ...mockGitifyNotification,
+            id: 'non-existent-id',
+          },
+        ],
+        mockSingleAccountNotifications,
+      );
+
+      expect(result[0].notifications.length).toBe(1);
+      expect(result[0].notifications[0].unread).toBe(true);
+    });
+
+    it('should skip notification removal if nothing to remove', () => {
+      expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
+
+      const result = removeNotificationsForAccount(
+        mockSingleAccountNotifications[0].account,
+        { ...mockSettings, delayNotificationState: false },
+        [],
+        mockSingleAccountNotifications,
+      );
+
+      expect(result[0].notifications.length).toBe(1);
+      expect(result[0].notifications[0]).toBe(
+        mockSingleAccountNotifications[0].notifications[0],
+      );
+    });
+
+    it('should not modify notifications when account UUID does not match', () => {
+      const result = removeNotificationsForAccount(
+        mockGitHubEnterpriseServerAccount, // Different account
+        { ...mockSettings, delayNotificationState: false },
+        [mockGitifyNotification],
+        mockSingleAccountNotifications,
+      );
+
+      expect(result[0].notifications.length).toBe(1);
+      expect(result[0].notifications[0]).toBe(
+        mockSingleAccountNotifications[0].notifications[0],
+      );
+    });
+
+    it('should mark as read and skip removal when fetchReadNotifications is enabled', () => {
+      expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
+
+      const result = removeNotificationsForAccount(
+        mockSingleAccountNotifications[0].account,
+        { ...mockSettings, fetchReadNotifications: true },
+        [mockGitifyNotification],
+        mockSingleAccountNotifications,
+      );
+
+      expect(result[0].notifications.length).toBe(1);
+      expect(result[0].notifications[0].unread).toBe(false);
+    });
+
+    it('should remove notifications when fetchReadNotifications is disabled', () => {
+      expect(mockSingleAccountNotifications[0].notifications.length).toBe(1);
+
+      const result = removeNotificationsForAccount(
+        mockSingleAccountNotifications[0].account,
+        { ...mockSettings, fetchReadNotifications: false },
+        [mockGitifyNotification],
+        mockSingleAccountNotifications,
+      );
 
-  it('should not modify notifications when account UUID does not match', () => {
-    const result = removeNotificationsForAccount(
-      mockGitHubEnterpriseServerAccount, // Different account
-      { ...mockSettings, delayNotificationState: false },
-      [mockGitifyNotification],
-      mockSingleAccountNotifications,
-    );
-
-    expect(result[0].notifications.length).toBe(1);
-    expect(result[0].notifications[0]).toBe(
-      mockSingleAccountNotifications[0].notifications[0],
-    );
+      expect(result[0].notifications.length).toBe(0);
+    });
   });
 });
diff --git a/src/renderer/utils/notifications/remove.ts b/src/renderer/utils/notifications/remove.ts
index 160d479a5..96f744ab2 100644
--- a/src/renderer/utils/notifications/remove.ts
+++ b/src/renderer/utils/notifications/remove.ts
@@ -6,10 +6,23 @@ import type {
 } from '../../types';
 import { getAccountUUID } from '../auth/utils';
 
+/**
+ * Determine if notifications should be removed from state or marked as read in-place.
+ *
+ * When `delayNotificationState` or `fetchReadNotifications` is enabled,
+ * notifications stay in the list with reduced opacity instead of being removed.
+ */
+export function shouldRemoveNotificationsFromState(
+  settings: SettingsState,
+): boolean {
+  return !settings.delayNotificationState && !settings.fetchReadNotifications;
+}
+
 /**
  * Remove notifications from the account notifications list.
  *
- * If delayNotificationState is enabled in settings, mark notifications as read instead of removing them.
+ * When `delayNotificationState` or `fetchReadNotifications` is enabled,
+ * notifications are marked as read instead of being removed from the list.
  */
 export function removeNotificationsForAccount(
   account: Account,
@@ -25,18 +38,20 @@ export function removeNotificationsForAccount(
     notificationsToRemove.map((notification) => notification.id),
   );
 
+  const shouldRemove = shouldRemoveNotificationsFromState(settings);
+
   return accountNotifications.map((accountNotifications) =>
     getAccountUUID(account) === getAccountUUID(accountNotifications.account)
       ? {
           ...accountNotifications,
-          notifications: settings.delayNotificationState
-            ? accountNotifications.notifications.map((notification) =>
+          notifications: shouldRemove
+            ? accountNotifications.notifications.filter(
+                (notification) => !notificationIDsToRemove.has(notification.id),
+              )
+            : accountNotifications.notifications.map((notification) =>
                 notificationIDsToRemove.has(notification.id)
                   ? { ...notification, unread: false }
                   : notification,
-              )
-            : accountNotifications.notifications.filter(
-                (notification) => !notificationIDsToRemove.has(notification.id),
               ),
         }
       : accountNotifications,