SCP Permission denied (publickey). on EC2 only when using -r flag on directories

The -i flag specifies the private key (.pem file) to use. If you don’t specify that flag (as in your first command) it will use your default ssh key (usually under ~/.ssh/).

So in your first command, you are actually asking scp to upload the .pem file itself using your default ssh key. I don’t think that is what you want.

Try instead with:

scp -r -i /Applications/XAMPP/htdocs/keypairfile.pem uploads/* ec2-user@publicdns

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