Messages showing phantom unread message count on Macbook (Messages in iCloud enabled) with no actual unread messages

I found that this was a recently deleted message. Go to View - Recently Deleted. On your dock, right click on the Message app and it should show which message it thinks is unread. I was able to find it in recently deleted. Right click on the deleted message and select restore. Now you can view the message and re-delete it.

This worked quickly for me:

In Mac Messages app, (1) select all conversations from the left side panel that shows all the people/phone numbers. To select just click the first name, then scroll down to last (oldest) name and shift-click. They should all be highlighted blue. (2) Cntrl-click any of the names. (3) In the contextual menu that pops up, click on "Mark as unread". Your badge count should shoot up to 100s or 1000s. (4) With all the names still selected, or re-select again, Cntrl-click any of the names. (5) In the contextual menu that pops up, click on "Mark as read". Your badge count should shoot down to zero. Process took about 2 minutes for me.

THANK YOU! I also tried everything else in this thread and nothing worked. Asking siri to read my unread messages and saying no every time she asked if I wanted to reply one by one was the only thing that worked. Thank you so much!

Thank you. Asking Siri to read unread messages solved the problem

I have found a solution to the problem.

1) On the MacBook (where this issue is happening), go to settings

2) Click on your Apple ID

3) iCloud

4) Messages in iCloud

5) Sync Now

Restarting my Macbook has always worked to clear the flag.

Remove from dock and putting back in dock also does work.

Try rebuilding your Spotlight Index...

1. 1. Choose Apple menu () > System Preferences, then click Spotlight.
2. Click the Privacy tab.
3. Drag the folder or disk that you want to index again to the list of locations that Spotlight is prevented from searching. Or click the Add (+) button and select the folder or disk to add.
4. To add an item to the Privacy tab, you must have ownership permissions for that item. To learn about permissions, choose Help from the Finder menu bar, then search for “permissions.”
5. From the same list of locations, select the folder or disk that you just added. Then click the Remove (–) button to remove it from the list.
6. Quit System Preferences. Spotlight will reindex the contents of the folder or disk.

Just wanted to add a share something! I tried literally everything listed on here and none of them worked. But I ended up checking reddit and found the solution right away!

Ask Siri on your mac to read unread messages and that should do the trick :)

Tell Siri on your Mac to "read my unread messages" and it do all the work for you!

SUGGESTION: put on your air pods or headphones before doing this, because it will read out loud your text messages and if your not home alone then you could be making audible your private conversations.

OMG! I've had that dang red unread bubble on my laptop for YEARS! I didn't do the terminal bit, but just removing iMessage from the dock and putting it back totally worked to clear it! THANK YOU!! (tears streaming down face emoji!!)

I tried absolutely everything. Finally, thanks to Reddit -- have Siri read all unread messages. Took me months to figure out, but she did it.

Asking siri to "Read all unread messages" works perfectly....

This worked! Simple, smooth, quick. No "terminal" work required.

I'm commenting on this to keep the thread alive - because this is the solution I needed. Thank you for providing this. You made the world a better place! For those with a one-button mouse, use control^click.