git fetch origin --prune doesn't delete local branches?

The various prune options (git remote update --prune, git remote prune, git fetch --prune) only delete remote-tracking branches.¹

You'll need to manually delete local branches you no longer want, or change or remove their upstream setting if the remote-tracking branch no longer exists. Note that each local branch can record a remote and/or branch that do not now, or even never did, exist. In this case Git mostly acts as if those local branches have no upstream set, except that since version 1.8.5, several commands report the upstream as "gone" or otherwise invalid, and may suggest using --unset-upstream.

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¹More precisely, they delete destination refs after doing the refspec mapping from the command line or fetch lines from the configuration. Hence, for fetch mirrors, they can delete local branches. Most clones are not set up as fetch mirrors, though.

There were some recent bug fixes for complex mappings, to make sure that Git did not prune a mapped branch in some cases when it should not. For any normal repository—ordinary clone or pure fetch mirror—these fixes have no effect; they matter only if you have complicated fetch configurations.

The following command chain can be used to delete local branches:

git branch --v | grep "\[gone\]" | awk '{print $1}' | xargs git branch -D

• git branch --v lists the local branches verbosely
• grep "[gone]" finds all the branches whose remote branch is gone
• awk '{print $1}' outputs only the name of the matching local branches
• xargs git branch -D deletes all the matching local branches

This should work on MacOS as well as *nix environments.

The command you want is

$ git remote prune origin

This question is almost word for word what you're looking for.