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Remember that you have to deactivate your Facebook account in order to see the option to deactivate your Messenger account.
This action can only be done on a mobile device.
To deactivate Messenger after you've deactivated your Facebook account:
iPhone, iPad and Android
- Open Messenger and tap your profile picture in the corner.
- Scroll down and tap Account settings.
- Tap Account ownership and control.
- Tap Deactivation and deletion.
- Tap Continue to Facebook account deactivation and deletion.
- Tap Continue to account deactivation.
- Enter your password and tap Continue.
To reactivate Messenger, log in with your username and password.