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This Google guide talks about configuring ones Gmail (e.g. me@gmail.com) to fetch emails from another mail service (e.g. me@myorganization.com) via POP3 into as well as being able to send emails as me@myorganization.com from Gmail.

But if you delete/move an email from within Gmail that was originally pulled over POP3, will Gmail also delete that message from the original me@myorganization.com mailbox, thereby syncing it?

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No, Gmail will not sync your changes on the origin server when using POP mail fetching, and as far as I know, no email client does this either. It’s simply not a feature of POP.

Your only option is to leave or delete your email on the origin server at the time Gmail retrieves your email. You can edit this by going into SettingsAccounts and Imports and clicking edit info next to the POP account in question:

Accounts and Imports

Then, uncheck Leave a copy of retrieved message on the server. to remove the original message:

Leave a copy of retrieved message on the server

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