Centralized Let’s Encrypt Management

Updated March 16, 2017 to reflect current webroot settings

Recently I set out to see how I could manage lets encrypt certificates from one central server, even though the actual websites didn’t live on that server. My reasoning was basically “This is how I did it with SSLMate, so let’s keep doing it” but it should also be helpful in situations where you have a cluster of webservers, and probably some other situations that I can’t think of at this time.

Before I get too in depth with how this all works, I’m going to define what I mean by two servers we have to work with:

  • Cert Manager: This is the server that actually runs Let’s Encrypt, where we run commands to issue certificates.
  • Client Server: This is the server serving the website, say… chrismarslender.com 😉

Additionally, I have a domain setup that I point to the Cert Manager. For the purposes of this article, lets just call it certmanager.mywebsite.com.

High Level Overview

At a high level, here’s how it works with the web root verification strategy:

  1. I set up nginx on the Cert Manager to listen for requests at certmanager.mywebsite.com, and if the request is for anything under the path /.well-known/ I serve up the file the request is asking for.
  2. On the client servers, I have a common nginx include that matches the /.well-known/ location, and proxies that request over to the certmanager.mywebsite.com server.

Nginx Configuration

Here’s what the configuration files look like, for both the Cert Manager Server as well as the common include for the client servers:

Cert Manager Nginx Conf:

server {
    listen 80;
    server_name certmanager.mywebsite.com;
    access_log /var/log/nginx/cert-manager.access.log;
    error_log /var/log/nginx/cert-manager.error.log;

    root /etc/letsencrypt/webroot;

    location /.well-known {
        try_files $uri $uri/ =404;

    location / {
        return 403;

Client Server Common Nginx Include:

location ~ /\.well-known {
    proxy_pass http://certmanager.mywebsite.com;

Issuing a Certificate

Now lets say I want to issue a certificate for chrismarslender.com – here is what the process would look like.
I’m assuming chrismarslender.com is already set up to serve the website on a client server by this point.

SSH to the Cert Manager server, and run the following command:

letsencrypt certonly -a webroot --webroot-path /etc/letsencrypt/webroot -d chrismarslender.com -d www.chrismarslender.com

Eventually, this command generates a verification file in the /etc/letsencrypt/live/.well-known/ directory, and then Let’s Encrypt tries to load the file to verify domain ownership at chrismarslender.com/.well-known/<file>.

Since the client server hosting chrismarslender.com is set up to proxy requests under /.well-known/ to the Cert Manager server (using the common include above), the file that was just created on the Cert Manager server is transparently served to Let’s Encrypt, and ownership of the domain is verified. Now, I have some fancy new certificates sitting in /etc/letsencrypt/live/chrismarslender.com

At this point, you just have to move the certificates to the final web server, reload nginx, and you’re in business.

In practice, I actually use ansible to manage all of this – I’ll work on a follow up post explaining how that all works as well, but generally I end up issuing SSL certificates as part of the site provisioning process on the Client Servers, in combination with `delegate_to`. Also, ansible makes steps like the moving of certificates to the final web server must less labor intensive 🙂

Things to Figure Out

I’m still trying to figure out the best strategy to keep the certificates updated. I can run the Let’s Encrypt updater on the Cert Manager server and get new certificates automatically, but since it’s not the web server that actually serves the websites, I need to figure out how I want to distribute new certificates to appropriate servers when they are updated. Feel free to comment if you have a brilliant idea 😉

13 thoughts on “Centralized Let’s Encrypt Management

  1. Hello Chris, have you figured out a way to deploy the certificates?

    I was thinking about NFS, it would be really transparent, but I would be adding an additional layer of problem, if the NFS goes down we’ve a problem.


    1. I haven’t had time to dig in and find a good solution for that yet, unfortunately. For now, I’m just issuing the certificates on the individual webservers and setting up the auto renew there.

    2. I decided to go down this route as well.

      I am on AWS and I’ve got 15,000 domains to secure. I am going to make use of Elastic File Storage (aws version of NFS) to host them.

      1. With nginx, if the underlying certificate changes, you need to restart the service to load up the new certificate. How are you planning on detecting changes to the certificates and restarting across all the servers?

        1. Hello cmmarslender,

          I think you don’t need to restart nginx. You can run “nginx reload” to re-load the certs without downtime.

          As far as detection goes: I am going to write a small service that checks new domains every 15 minutes and updates the configuration & issue reload command.

          I could not found any better way. New domains gets added/removed every day on my platform 🙁

          1. Ah yeah – reload or restart, my point was more or less the same. I was curious if you had found a better solution for detecting changes and issuing the command to reload.

  2. incron (Linux only) uses inotify to trigger commands. Using incron, you can detect the cert file changing and use scp/ssh to distribute the key(s) and reload nginx.

  3. Integrate with Ansible.

    – CertManager will get new Certificates periodically and then let Ansible to do the remaining Jobs

    – Ansbile copy new certificate to the destination server
    – Ansible restart web services in destination server

  4. Great article – and excellent input about Ansible, Dijeesh.
    I’ll be looking into a solution involving Puppet – anyone having experience with such a setup?

  5. Great article Chri! Please correct me if I am wrong but… how smart it is to set nginx root directory as your certificate root directory?

    I think this is really dangerous thing to do: “root /etc/letsencrypt/live;”

    Any small mistake in the future will open up all of your certs to outside world 😀

    1. This is a good point. In the configuration provided in the article, the location / block that returns a 403 (forbidden) was intended to prevent this from happening, but I’ve since changed how I do this a bit to avoid that requirement. My location block looks like this now:

      location ~ /\.well-known {
      	root /etc/letsencrypt/webroot;
      	try_files $uri $uri/ =404;

      Defining the root inside of the location block leaves you free to set the other root to anything you desire. I’ve updated the article to reflect not using the /live directory.

  6. I am still torn on how to automate the distribution of the renewed certs. I have configured a cron job to automatically renew the lets encrypt cert; but then i dont wish to stay using ansible to distribute the files. I was considering using a repo on a private git server secured by ssh keys and pushing the entire LE folder structure as a new commit whenever a new version of the certs is available. Then from the client side I can stay polling for new commits and pull. My concern with this approach is security then..thoughts anyone?

Leave a Reply

Your email address will not be published. Required fields are marked *