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:/var/www/html/uploads

Even if above solutions don't work, check permissions to destination file of aws ec2 instance. May be you can try with- sudo chmod 777 -R destinationFolder/*

transferring file from local to remote host

scp -i (path of your key) (path for your file to be transferred) (username@ip):(path where file to be copied)

e.g scp -i aws.pem /home/user1/Desktop/testFile   ec2-user@someipAddress:/home/ec2-user/

P.S. - ec2-user@someipAddress of this ip address should have access to the destination folder in my case /home/ec2-user/