How to Renew SSL Certificates with Certbot in Docker (Works with Azure or AWS Domains)

If you’re running Nginx in a Docker container (for example, on a Raspberry Pi or a self-hosted server), and your domains are managed through Azure DNS or AWS Route 53, this step-by-step guide will show you how to automatically renew Let’s Encrypt SSL certificates using Certbot with the webroot method.

1. Prerequisites

Before getting started, make sure you have:

• Docker and docker-compose installed
• Certbot installed on the host system (not inside the container)
• Nginx running inside a Docker container
• Access to your DNS zone (Azure or AWS)
• A domain pointing to your public IP (check with https://whatismyip.com)

2. Your docker-compose.yml Setup

Here’s a sample docker-compose.yml configuration for Nginx:

version: '3'
services:
  nginx:
    image: nginx:latest
    container_name: nginx
    volumes:
      - ./nginx.conf:/etc/nginx/conf.d/default.conf
      - /usr/share/nginx/html:/usr/share/nginx/html
      - /etc/letsencrypt:/etc/letsencrypt:ro
    ports:
      - "80:80"
      - "443:443"
    networks:
      - default
      - yourproject_wp_net

networks:
  yourproject_wp_net:
    external: true

Make sure to mount /usr/share/nginx/html since Certbot will place temporary challenge files there.

3. First-time Certificate Issuance with Certbot (using webroot)

Use the webroot method to avoid stopping Nginx and prevent port conflicts:

sudo certbot certonly --webroot \
  -w /usr/share/nginx/html \
  -d yourdomain.com -d www.yourdomain.com \
  --cert-name yourdomain.com

This command will request a new certificate if everything is configured correctly.
⚠️ IMPORTANT: Make sure yourdomain.com and www.yourdomain.com point to your public IP. Use dig yourdomain.com +short to confirm.

4. Reloading Nginx When Certificates Are Renewed

Create this script at:

/etc/letsencrypt/renewal-hooks/deploy/reload_nginx_docker.sh

With the following contents:

#!/bin/bash
# Script to reload Nginx inside Docker

echo "Reloading Nginx container..."
docker-compose -f /path/to/your/docker-compose.yml exec nginx nginx -s reload || \
docker-compose -f /path/to/your/docker-compose.yml restart nginx

Make it executable:

sudo chmod +x /etc/letsencrypt/renewal-hooks/deploy/reload_nginx_docker.sh

5. Automate Renewals with Cron

Edit your system’s crontab:

sudo crontab -e

Add this line to run every midnight:

0 0 * * * certbot renew --webroot -w /usr/share/nginx/html

Certbot will run your reload script automatically after a successful renewal.

6. Verify That Everything Works

Run a dry run to simulate the renewal process:

sudo certbot renew --dry-run

Also, test if the challenge path is being served:

curl http://yourdomain.com/.well-known/acme-challenge/test.txt

Manually create that file inside /usr/share/nginx/html/.well-known/acme-challenge/ to verify Nginx is exposing it.

7. If Your Domain is Managed in AWS Route 53

If you use AWS Route 53 instead of Azure, you can use Certbot’s DNS plugin:

sudo certbot -a dns-route53 -d yourdomain.com -d www.yourdomain.com

Make sure your AWS credentials are configured in ~/.aws/credentials.
This is helpful if you can’t expose ports 80/443 due to firewalls or NAT restrictions.

⚠️ 8. Common Issues and Fixes

Error	Cause	Solution
bind: address already in use	System Nginx running outside Docker	Stop it with sudo systemctl stop nginx
Some challenges have failed	Domain doesn’t point to your IP	Double-check DNS records and IP
Unable to find a Route53 hosted zone	Domain not in AWS	Use webroot method or DNS plugin for Azure

Conclusion

With this setup:

• Your SSL certificates will renew automatically via certbot renew
• Your Nginx container will reload itself without downtime
• Works with Azure or AWS domains
• You retain full control without relying on external Certbot containers

Did This Guide Help You?

Leave a comment or share your setup! Hopefully, this saved you hours of debugging like it did for me. 😉