Remove website Notifications in Systems Settings but doesn't show up in Safari

Thank you so much. I had the same problem. Websites remained in the Notifications of the System Settings, but did not appear in the Notifications Settings of Safari. By deleting the specific folders in /Users/username/Library/Caches/com.apple.Safari/RemoteNotifications/filenames and then a restart of the System Settings, the entries disappeared. Great!

It sounds frustrating that those website notifications persist in your System Settings without showing up in Safari’s settings for management. Since you've already tried several methods, here are a few additional steps you could take: First, clear Safari's caches and website data by going to Safari > Settings > Privacy > Manage Website Data, and clicking “Remove All” to reset any lingering notifications. Next, check for any installed profiles under System Settings > Privacy & Security > Profiles and remove them if they’re from websites. You can also use Terminal to reset Safari notifications by entering the command `defaults delete com.apple.Safari PushNotifications` and restarting your MacBook Pro. Additionally, consider reviewing the Notification Center database using Terminal, though this is more advanced and should be done cautiously. If none of these methods work, it might be necessary to look into a fresh macOS installation or contact Apple Support for more help.

There is another file that seems to store the list: ~/Library/Preferences/com.apple.ncprefs.plist.

It should be possible to delete specific entries from that file but I have no idea of the consequences. Same if you were to delete the entire file.

If you want to see the content of the file, open Terminal (in the Applications > Utilities folder) and execute this command:

defaults read ~/Library/Preferences/com.apple.ncprefs.plist

Or you could use a plist file editor to view it and edit it. I used Xcode (which is overkill for this task) to view the content of the file and I see that I could delete elements from the "apps" array.

If you were to edit the file or delete it, I'm pretty sure a reboot would be necessary.

Try the solution posted in this thread: I cannot delete website from notification… - Apple Community

Mullmuzzler1979 wrote:

That did not work. I deleted them from the location /Users/username/Library/Caches/com.apple.Safari/RemoteNotifications/filenames but it made no difference. The websites still show up in the System Settings > Notifications even though the Safari Settings > Notifications list is empty.

You'll need to restart your computer too. Any kind of low-level hacking like this will require a restart.

Look for some other suggestions in that thread I mentioned. At one point, I suggested using the Terminal command: "sudo tccutil reset All". You might need to do both of these to clear out the notifications.

In System Settings > Notifications, right-click the website and choose to reinitialize the notifications. This should remove the website from the list.