How to Secure Nginx with Let’s Encrypt SSL/TLS on Ubuntu Using Certbot

ByAkensai

Learning how to secure Nginx with Let’s Encrypt SSL/TLS on Ubuntu using Certbot is one of the most important skills for any server administrator. HTTPS is no longer optional. Browsers flag HTTP sites as “Not Secure,” and search engines rank secure sites higher. Let’s Encrypt gives you a free, trusted SSL certificate. Certbot automates the entire process. By the end of this tutorial, you’ll have a fully secured Nginx server with automatic certificate renewal. This guide works on Ubuntu 20.04 and 22.04 LTS.

Prerequisites to Secure Nginx with Let’s Encrypt SSL/TLS on Ubuntu Using Certbot

Before you start, make sure you have everything in place. Skipping these steps will cause the process to fail.

You will need:

– A server running Ubuntu 20.04 or 22.04 LTS
– Nginx installed and running
– A registered domain name pointing to your server’s IP address
– Root or sudo access to the server
– Port 80 and 443 open in your firewall

Assumed knowledge: You should be comfortable with the Linux command line. You don’t need to be an expert, but basic terminal skills are required.

Estimated time: 15–20 minutes.

First, confirm your domain’s DNS A record points to your server. You can check this with:

dig +short yourdomain.com

The output should return your server’s public IP address. If it doesn’t, wait for DNS propagation before continuing. Certificate issuance will fail if Let’s Encrypt can’t reach your domain.

Also confirm Nginx is running:

sudo systemctl status nginx

You should see active (running) in the output. If Nginx isn’t running, start it with sudo systemctl start nginx.

Step-by-Step Guide to Secure Nginx with Let’s Encrypt SSL/TLS on Ubuntu Using Certbot

This event shares similarities with: How to Protect Your Linux Server From Brute-force Attacks with Fail2ban

Follow these steps carefully. Each one builds on the last.

Step 1: Update your system packages

Always start with a system update. This ensures you install the latest version of Certbot.

sudo apt update && sudo apt upgrade -y

Step 2: Install Certbot and the Nginx plugin

Ubuntu’s package repositories include Certbot. Install it along with the Nginx plugin:

sudo apt install certbot python3-certbot-nginx -y

The python3-certbot-nginx plugin lets Certbot automatically edit your Nginx configuration. This saves you from manually updating config files.

Step 3: Configure your Nginx server block

Certbot needs a server block with your domain name to work correctly. Open your Nginx config file:

sudo nano /etc/nginx/sites-available/yourdomain.com

Make sure the server_name directive includes your domain:

server {
    listen 80;
    server_name yourdomain.com www.yourdomain.com;

    root /var/www/yourdomain.com/html;
    index index.html index.php;
}

Save the file and test your Nginx configuration:

sudo nginx -t

If you see syntax is ok, reload Nginx:

sudo systemctl reload nginx

Step 4: Allow HTTPS through the firewall

If you’re using UFW, open ports 80 and 443:

sudo ufw allow 'Nginx Full'
sudo ufw delete allow 'Nginx HTTP'

The first command opens both HTTP and HTTPS. The second removes the old HTTP-only rule.

Step 5: Run Certbot to obtain your SSL certificate

Now run Certbot with the Nginx plugin. Replace yourdomain.com with your actual domain:

sudo certbot --nginx -d yourdomain.com -d www.yourdomain.com

Certbot will ask for your email address and ask you to agree to the Terms of Service. It then contacts Let’s Encrypt, verifies your domain, and installs the certificate. You can learn more about how this process works in the Let’s Encrypt documentation.

Step 6: Verify the certificate installation

Open a browser and navigate to https://yourdomain.com. You should see a padlock icon in the address bar. You can also check via the command line:

sudo certbot certificates

This shows all installed certificates, their domains, and expiry dates.

Step 7: Test automatic renewal

Let’s Encrypt certificates expire after 90 days. Certbot sets up a systemd timer to renew them automatically. Test the renewal process with a dry run:

sudo certbot renew --dry-run

If the dry run completes without errors, automatic renewal is working. You don’t need to do anything else. Certbot handles renewals for you.

Troubleshooting Common Issues When You Secure Nginx with SSL/TLS Using Certbot

Even with careful setup, things can go wrong. Here are the most common issues and how to fix them.

Error: “Could not bind to IPv4 or IPv6”

This means something is already using port 80. Stop Apache if it’s running:

sudo systemctl stop apache2

Then run Certbot again.

Error: “No names were found in your configuration files”

Certbot can’t find your domain in the Nginx config. Double-check your server_name directive matches the domain you passed with -d.

Error: “Connection timed out during challenge”

Let’s Encrypt couldn’t reach your server on port 80. Check your firewall rules:

sudo ufw status

Make sure port 80 is open. Also check your cloud provider’s security group settings if you’re on AWS, DigitalOcean, or similar platforms.

Certificate not renewing automatically

Check the Certbot timer status:

sudo systemctl status certbot.timer

If it’s inactive, enable it:

sudo systemctl enable certbot.timer
sudo systemctl start certbot.timer

Mixed content warnings

After enabling HTTPS, your browser may warn about mixed content. This happens when your site loads HTTP resources like images or scripts. Update all internal links to use HTTPS. If you’re running WordPress, the Nginx HTTPS server configuration guide can help you set up proper redirects.

You can also add an HTTP to HTTPS redirect in your Nginx config:

server {
    listen 80;
    server_name yourdomain.com www.yourdomain.com;
    return 301 https://$host$request_uri;
}

This forces all HTTP traffic to redirect to HTTPS automatically.

Conclusion

You now know how to secure Nginx with Let’s Encrypt SSL/TLS on Ubuntu using Certbot. Your server serves traffic over HTTPS. Your certificate renews automatically. Visitors see a padlock instead of a security warning. That’s a meaningful improvement for both security and trust.

From here, you can go further. Consider adding HTTP Strict Transport Security (HSTS) headers to your Nginx config. You can also look into OCSP stapling to speed up SSL handshakes. If you’re running WordPress on this server, make sure your site URL is updated to use HTTPS in the WordPress settings. These extra steps strengthen your server’s security posture and improve performance.

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