How To Secure Nginx with Let's Encrypt on Ubuntu 16.04

How To Secure Nginx with Let's Encrypt on Ubuntu 16.04
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Ubuntu 16.04


Let’s Encrypt is a Certificate Authority (CA) that provides an easy way to obtain and install free TLS/SSL certificates, thereby enabling encrypted HTTPS on web servers. It simplifies the process by providing a software client, Certbot, that attempts to automate most (if not all) of the required steps. Currently, the entire process of obtaining and installing a certificate is fully automated on both Apache and Nginx.

In this tutorial, you will use Certbot to obtain a free SSL certificate for Nginx on Ubuntu 16.04 and set up your certificate to renew automatically.

This tutorial uses the default Nginx configuration file instead of a separate server block file. We recommend creating new Nginx server block files for each domain because it helps to avoid some common mistakes and maintains the default files as a fallback configuration as intended. If you want to set up SSL using server blocks instead, you can follow this Nginx server blocks with Let’s Encrypt tutorial.


To follow this tutorial, you will need:

  • One Ubuntu 16.04 server set up by following this initial server setup for Ubuntu 16.04 tutorial, including a sudo non-root user and a firewall.
  • A fully registered domain name. This tutorial will use example.com throughout. You can purchase a domain name on Namecheap, get one for free on Freenom, or use the domain registrar of your choice.
  • Both of the following DNS records set up for your server. You can follow this hostname tutorial for details on how to add them.
    • An A record with example.com pointing to your server’s public IP address.
    • An A record with www.example.com pointing to your server’s public IP address.
  • Nginx installed by following How To Install Nginx on Ubuntu 16.04.

Step 1 — Installing Certbot

The first step to using Let’s Encrypt to obtain an SSL certificate is to install the Certbot software on your server.

Certbot is in very active development, so the Certbot packages provided by Ubuntu tend to be outdated. However, the Certbot developers maintain a Ubuntu software repository with up-to-date versions, so we’ll use that repository instead.

First, add the repository.

  1. sudo add-apt-repository ppa:certbot/certbot

You’ll need to press ENTER to accept. Then, update the package list to pick up the new repository’s package information.

  1. sudo apt-get update

And finally, install Certbot’s Nginx package with apt-get.

  1. sudo apt-get install python-certbot-nginx

Certbot is now ready to use, but in order for it to configure SSL for Nginx, we need to verify some of Nginx’s configuration.

Step 2 — Setting up Nginx

Certbot can automatically configure SSL for Nginx, but it needs to be able to find the correct server block in your config. It does this by looking for a server_name directive that matches the domain you’re requesting a certificate for.

If you’re starting out with a fresh Nginx install, you can update the default config file. Open it with nano or your favorite text editor.

  1. sudo nano /etc/nginx/sites-available/default

Find the existing server_name line and replace the underscore, _, with your domain name:

. . .
server_name example.com www.example.com;
. . .

Save the file and quit your editor.

Then, verify the syntax of your configuration edits.

  1. sudo nginx -t

If you get any errors, reopen the file and check for typos, then test it again.

Once your configuration’s syntax is correct, reload Nginx to load the new configuration.

  1. sudo systemctl reload nginx

Certbot will now be able to find the correct server block and update it. Next, we’ll update our firewall to allow HTTPS traffic.

Step 3 — Allowing HTTPS Through the Firewall

If you have the ufw firewall enabled, as recommended by the prerequisite guides, you’ll need to adjust the settings to allow for HTTPS traffic. Luckily, Nginx registers a few profiles with ufw upon installation.

You can see the current setting by typing:

  1. sudo ufw status

It will probably look like this, meaning that only HTTP traffic is allowed to the web server:

Status: active To Action From -- ------ ---- OpenSSH ALLOW Anywhere Nginx HTTP ALLOW Anywhere OpenSSH (v6) ALLOW Anywhere (v6) Nginx HTTP (v6) ALLOW Anywhere (v6)

To additionally let in HTTPS traffic, we can allow the Nginx Full profile and then delete the redundant Nginx HTTP profile allowance:

  1. sudo ufw allow 'Nginx Full'
  2. sudo ufw delete allow 'Nginx HTTP'

Your status should look like this now:

  1. sudo ufw status
Status: active To Action From -- ------ ---- OpenSSH ALLOW Anywhere Nginx Full ALLOW Anywhere OpenSSH (v6) ALLOW Anywhere (v6) Nginx Full (v6) ALLOW Anywhere (v6)

We’re now ready to run Certbot and fetch our certificates.

Step 4 — Obtaining an SSL Certificate

Certbot provides a variety of ways to obtain SSL certificates, through various plugins. The Nginx plugin will take care of reconfiguring Nginx and reloading the config whenever necessary:

  1. sudo certbot --nginx -d example.com -d www.example.com

This runs certbot with the --nginx plugin, using -d to specify the names we’d like the certificate to be valid for.

If this is your first time running certbot, you will be prompted to enter an email address and agree to the terms of service. After doing so, certbot will communicate with the Let’s Encrypt server, then run a challenge to verify that you control the domain you’re requesting a certificate for.

If that’s successful, certbot will ask how you’d like to configure your HTTPS settings.

Please choose whether or not to redirect HTTP traffic to HTTPS, removing HTTP access. ------------------------------------------------------------------------------- 1: No redirect - Make no further changes to the webserver configuration. 2: Redirect - Make all requests redirect to secure HTTPS access. Choose this for new sites, or if you're confident your site works on HTTPS. You can undo this change by editing your web server's configuration. ------------------------------------------------------------------------------- Select the appropriate number [1-2] then [enter] (press 'c' to cancel):

Select your choice then hit ENTER. The configuration will be updated, and Nginx will reload to pick up the new settings. certbot will wrap up with a message telling you the process was successful and where your certificates are stored:

IMPORTANT NOTES: - Congratulations! Your certificate and chain have been saved at /etc/letsencrypt/live/example.com/fullchain.pem. Your cert will expire on 2017-10-23. To obtain a new or tweaked version of this certificate in the future, simply run certbot again with the "certonly" option. To non-interactively renew *all* of your certificates, run "certbot renew" - Your account credentials have been saved in your Certbot configuration directory at /etc/letsencrypt. You should make a secure backup of this folder now. This configuration directory will also contain certificates and private keys obtained by Certbot so making regular backups of this folder is ideal. - If you like Certbot, please consider supporting our work by: Donating to ISRG / Let's Encrypt: https://letsencrypt.org/donate Donating to EFF: https://eff.org/donate-le

Your certificates are downloaded, installed, and loaded. Try reloading your website using https:// and notice your browser’s security indicator. It should indicate that the site is properly secured, usually with a green lock icon. If you test your server using the SSL Labs Server Test, it will get an A grade.

Let’s finish by testing the renewal process.

Step 5 — Verifying Certbot Auto-Renewal

Let’s Encrypt’s certificates are only valid for ninety days. This is to encourage users to automate their certificate renewal process. The certbot package we installed takes care of this for us by running ‘certbot renew’ twice a day via a systemd timer. On non-systemd distributions this functionality is provided by a script placed in /etc/cron.d. This task runs twice a day and will renew any certificate that’s within thirty days of expiration.

To test the renewal process, you can do a dry run with certbot:

  1. sudo certbot renew --dry-run

If you see no errors, you’re all set. When necessary, Certbot will renew your certificates and reload Nginx to pick up the changes. If the automated renewal process ever fails, Let’s Encrypt will send a message to the email you specified, warning you when your certificate is about to expire.


In this tutorial, you installed the Let’s Encrypt client certbot, downloaded SSL certificates for your domain, configured Nginx to use these certificates, and set up automatic certificate renewal. If you have further questions about using Certbot, their documentation is a good place to start.

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hi! i write do.co/docs now, but i used to be the senior tech editor publishing tutorials here in the community.

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Watch out to the ssl-params.conf where you set X-Frame-Options to DENY. It will completely disable opening a page in frame or iframe, result will be that many reverse proxies, for example Deluge WebUI will not work, just as ownCloud will be limited too.

A common and recommended setting is to set it to SAMEORIGIN, that will still be pretty much safe to prevent Clickjacking, but it will allow functionality.

add_header X-Frame-Options SAMEORIGIN;

Hi @manicas - great tutorial, but they’ve changed all the names and now it’s called Certbot; there’s also an nginx plugin now, too!

See https://certbot.eff.org/docs/using.html#nginx :)

For those wondering about doing this for a subdomain, I just got this working properly.

toplevel.com == your top level domain sub.toplevel.com == your sub domain

  1. When running the certonly step implement your top level and subdomains like this if they are separate directories like mine. Obviously, you’ll want this all on one line. I broke it out a little bit so it would be easier to see what’s happening.
letsencrypt certonly --webroot 
-w /var/www/mytoplevel.com/html/ 
    -d www.mytoplevel.com 
    -d mytoplevel.com 
-w /var/www/sub.mytoplevel.com/html 
    -d sub.mytoplevel.com
  1. Setup server blocks appropriately. This is just how I have mine setup, and it’s working correctly. I followed this guide before running letsencrypt

Default Site

server {
        listen 80 default_server;
        listen [::]:80 default_server;

        root /var/www/html;

        # Add index.php to the list if you are using PHP
        index index.php index.html index.htm index.nginx-debian.html;

        server_name _;		
		# other configuration below

Top level domain in /etc/nginx/sites-available/toplevel.com

server {
        listen 80;
        listen [::]:80;
        server_name toplevel.com www.toplevel.com;
        return 301 https://$server_name$request_uri;

server {
        # SSL configuration

        listen 443 ssl http2 default_server;
        listen [::]:443 ssl http2 default_server;
        include snippets/ssl-toplevel.com.conf;
        include snippets/ssl-params.conf;

        root /var/www/toplevel.com/html;

        # Add index.php to the list if you are using PHP
        index index.php index.html index.htm index.nginx-debian.html;

        server_name toplevel.com www.toplevel.com;
		# other configuration below

Sub domain in /etc/nginx/sites-available/sub.toplevel.com

server {
        listen 80;
        listen [::]:80;
        server_name sub.toplevel.com;
        return 301 https://$server_name$request_uri;

server {
        # SSL configuration

        listen 443 ssl http2;
        listen [::]:443 ssl http2;
        include snippets/ssl-toplevel.com.conf;  # NOTE that this is the same file as the top level domain based on the tutorial
        include snippets/ssl-params.conf;

        root /var/www/sub.toplevel.com/html;

        # Add index.php to the list if you are using PHP
        index index.php index.html index.htm index.nginx-debian.html;

        server_name sub.toplevel.com;

		# other configuration below
  1. I am not an Nginx or encryption expert. I got it working by trying to piece things together from the different tutorials. Any questions you have might be better answered by those that are more experienced than I.

Thanks for the great tutorial.

I was able to install the certificate using the letsencrypt version in the 16.04 repos. So, instead of cloning the git repo, I was able to just apt-get install letsencrypt

Consequently, all the ./letsencrypt commands become sudo letsencrypt

In case it helps someone else, one issue I ran into while using these instructions with the “Ubuntu LEMP on 16.04” distribution is that its active server file is /etc/nginx/sites-enabled/digitalocean (symlinked to /etc/nginx/sites-available/digitalocean). Modifying /etc/nginx/sites-available/default would thus have no effect on the live server.

Simple fix:

    sudo rm /etc/nginx/sites-enabled/digitalocean
    sudo ln -s /etc/nginx/sites-available/default /etc/nginx/sites-enabled

I did every thing. But not taking A+ rating. It’s A. How can I fix it?

I’m having a problem. I was able to setup ssl, but my site now only shows the “Welcome to nginx!” page. (Before I setup ssl, I did see my files) I assumed the root was changed to /usr/share/nginx/html I’m a noob so I have no clue what to do. Placing “root /var/www/html” in the config file doesn’t do anything. Running Ubuntu LEMP on 16.04. Let me know if you need more info.

I encountered the follwing problem

[warn] “ssl_stapling” ignored, issuer certificate not found

SSL is working fine. I’m trying to get HTTP2 working on firefox.

You can add lets encrypt directly in 16.04 using apt-get install letsencrypt

Thanks for sharing, can you please comment on the two following topics?

  1. You are referring to initial server setup for Ubuntu 16.04 tutorial - which ends in 404.
  2. Following the (your) 14.04 security guides the root account has no remote ssh access. I am therefore logging in with “remoteuser” (just an example). onced logged-in I do require to enter a password for being able to execute commands with sudo permission.

Question 1: Have there been changes to 14.04 and if so: when will the referenced article be available?

Question 2: Shouldn´t nginx also run with its own permissions? If so, does that require any tweaks to the above guide?

Question 3: Under which permission are the cron jobs executed following the above guide? If root, would it make sense to have cron jobs run under a different account? And if that is the case and assuming nginx also have its own permissions under which it is running, does that somehow require additional tweaks to you guide?

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