By default, MobaXterm uses its own home directory:
C:\Users\UserName\Documents\MobaXterm\home
Therefore, its SSH folder:
~/.ssh
is different from the Windows SSH folder:
C:\Users\UserName.ssh
This can lead to different SSH keys and configuration files being used by MobaXterm, Windows OpenSSH, Git, and VS Code.
Solution
First, if need copy the existing MobaXterm SSH files to the Windows SSH folder:
mkdir -p /drives/c/Users/UserName/.ssh
cp -a ~/.ssh/. /drives/c/Users/UserName/.ssh/
Verify the result:
diff -qr ~/.ssh /drives/c/Users/UserName/.ssh
Files reported as existing only in the Windows folder are usually pre-existing Windows keys or configuration files and are not necessarily a problem.
Then open:
MobaXterm → Settings → Configuration → General
Change Terminal home directory to:
C:\Users\UserName
Leave Terminal root (/) directory unchanged.
Restart MobaXterm and verify:
echo “$HOME”
ls -la ~/.ssh
MobaXterm and Windows will now use the same SSH folder:
C:\Users\UserName.ssh