How to Set Up SSH Key Authentication in PuTTY (Without the Password Hassle)

If you've been typing your SSH password every single time you connect to your server, you're not alone. Most people start there. But here's the thing: using SSH keys is not only more secure, it also saves you from that repetitive password dance. Once it's set up, you just click and you're in.

The confusion usually comes from mixing up two different types of keys. Your server already has its own host keys (those files you found in Webmin), but those aren't what you need. What you actually need is a user key pair - one that belongs to you, not the server.

What You're Actually Looking For

Think of SSH keys like a lock and key system. The server has its own keys to prove it's really your server (those host keys you found), but you need your own personal key pair to prove you're really you.

Here's what that key pair looks like:

• Private key: stays on your computer, never share it

• Public key: goes on the server, totally safe to copy around

The private key is what PuTTY will use on your end. The public key gets added to your server's authorized list. When you connect, they do a handshake that proves you have the matching private key, without ever sending the actual key over the network.

Creating Your Key Pair with PuTTYgen

PuTTYgen comes bundled with PuTTY, so you already have it. Here's how to create your keys:

1. Open PuTTYgen (just search for it in your Windows start menu)

2. Leave the settings at "RSA" and "2048 bits" - that's perfectly fine for most use cases

3. Click "Generate" and move your mouse around randomly in the blank area. Yes, really. It uses that randomness to make your key more secure

4. Once it's done, you'll see a long string of text in the box labeled "Public key for pasting into OpenSSH authorized_keys file"

5. Save your private key: Click "Save private key" and put it somewhere safe on your computer. You might get a warning about not using a passphrase - adding one is more secure, but optional

6. Copy that public key text from the box (you'll need it in a minute)

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Getting That Public Key onto Your Server

Now you need to tell your server "hey, this public key is allowed to log in as me." The easiest way is through the command line:

1. Connect to your server the old way (with your password) using PuTTY

2. Run these commands:

mkdir -p ~/.ssh
chmod 700 ~/.ssh
nano ~/.ssh/authorized_keys

3. Paste your public key (the one you copied from PuTTYgen) into this file

4. Press Ctrl+X, then Y, then Enter to save

5. Set the right permissions:

chmod 600 ~/.ssh/authorized_keys

If you're doing this for a specific virtual host user (not root), just log in as that user first before running these commands. Each user gets their own authorized_keys file.

Connecting with PuTTY Using Your New Key

Almost there. Now you need to tell PuTTY to actually use that private key:

1. Open PuTTY

2. Enter your server address like normal

3. In the left menu, go to Connection → SSH → Auth

4. Click "Browse" next to "Private key file for authentication"

5. Select the .ppk file you saved earlier

6. Go back to "Session" at the top, save this profile so you don't have to browse for the key every time

7. Click "Open" to connect

You should connect without being asked for a password. If it still asks, double-check that you pasted the public key correctly on the server and that the file permissions are right.

Why This Matters Beyond Convenience

Password-based authentication has some real weaknesses. Someone can try thousands of password combinations (brute force attacks). Passwords can be intercepted if you're on a compromised network. And let's be honest, most of us reuse passwords more than we should.

With key authentication, all of that goes away. The private key never leaves your machine, and the math behind RSA encryption makes it practically impossible to fake. Even if someone intercepts your connection, they can't replay it or figure out your private key.

Quick Troubleshooting If Things Go Wrong

"Server refused our key": Your public key probably isn't in the right format or location. Make sure you pasted it into ~/.ssh/authorized_keys and not somewhere else.

PuTTY still asks for a password: Check that you actually selected the private key file in PuTTY's Auth settings before connecting.

"Couldn't load private key": You might be trying to load the public key instead of the private key, or the file got corrupted. Generate a fresh pair if needed.

Permission denied errors: SSH is picky about file permissions for security reasons. The .ssh folder should be 700, and authorized_keys should be 600.

One More Thing About Multiple Users

You asked about whether only root can have keys - nope, every user on your system can have their own key pairs. That's actually the recommended approach. Generate a key pair for each user account you need to access, and add each public key to that specific user's ~/.ssh/authorized_keys file.

So if you have a user called "webadmin" for one of your virtual hosts, SSH in as webadmin (with password), then add the public key to /home/webadmin/.ssh/authorized_keys. Each user's home directory has its own .ssh folder.

The host keys you found in Webmin are something different entirely - those are the server identifying itself to clients, not users authenticating to the server. That's why trying to use those files didn't work.

Now you can connect to your Debian server without fumbling for passwords every time. Set it up once, use it forever.