You can enable 2FA for SFTP Gateway using Google Authenticator. The instructions are based on this article, but are slightly adapted for use with SFTP Gateway.

Install Google Authenticator:

sudo yum install google-authenticator -y

Run the following command as the ec2-user (do not run it as root):

google-authenticator <<< $'y\ny\ny\nn\ny\n'

This will generate a file /home/ec2-user/.google_authenticator. It also uses an answer file that answers 5 questions as y (except for the 4th question).

You should also see a URL that looks like this: https://www.google.com/chart?chs=200x200&chld=M|0&cht=qr&chl=otpauth://totp/ec2-user@ip-172-31-11-130%3Fsecret%3DHA774ARZXPMD6VBC

Navigate to this url, and scan the barcode with your Google Authenticator app.

Next, run this command to edit the file:

sudo vi /etc/pam.d/sshd

Comment out the second line:

#auth       substack     password-auth

And append this line to the end:

auth required pam_google_authenticator.so secret=/home/${USER}/key/.google_authenticator

This line basically says to look for the file /home/<username>/key/.google_authenticator when performing 2FA. The key directory is the secret to making this all work, which I'll explain later on.

Next, move the .google_authenticator file to the key subdirectory:

cd /home/ec2-user
mkdir key && mv .google_authenticator $_

Make sure newly created users inherit this file as well:

sudo mkdir /etc/skel/key 
sudo cp -a /home/ec2-user/key/.google_authenticator /etc/skel/key 

(Note: if there are any existing users, make sure the ./key/.google_authenticator is copied to their home directory as well)

Next, edit the sshd_config file:

sudo vi /etc/ssh/sshd_config

(Un)comment the following lines, so that it looks like this:

ChallengeResponseAuthentication yes
#ChallengeResponseAuthentication no

And add the following line above the Match group sftponly section:

AuthenticationMethods publickey,keyboard-interactive

Note: This line needs to be above the Match group sftponly section!

Finally, restart sshd:

sudo service sshd restart

Now, try to SSH in as the ec2-user. You should be prompted for a Verification code.

Then, create an SFTP user (addsftpuser). When you try to connect, it should prompt you for a Verification code as well:

sftp -i robtest.key robtest@<ip address>
Verification code: 
Connected to <ip address>.
sftp> 

Explanation about the key subfolder

SFTP over OpenSSH requires that root have sole ownership of the ChrootDirectory.

Google Authenticator requires that the <user> own the .google_authenticator file, as well as its parent folder.

To avoid this conflict, we place the .google_authenticator file within a subfolder called key, which is owned by the user.