Initially you have to init the certbot and get the certificate manually.

# Directories used:
/var/www 
/var/www/certbot # handshake sites from certbot
/etc/letsencrypt # certificates are stored here

# Initialize Certbot:
docker run --rm -ti \
  -v /var/www:/var/www \
  -v /etc/letsencrypt:/etc/letsencrypt \
certbot/certbot certonly --webroot -w /var/www/certbot -d <yor-domain-name> --email your.email@something.com 

The letsencrypt and the www directory must be mounted on both containers. Certbot will check the certificates every 12h and nginx must reload the configuration periodically.

  nginx:
    image: nginx:1.17.8
    ports:
      - 80:80
      - 443:443
    volumes:
      - /var/www:/var/www
      - /etc/nginx.conf:/etc/nginx/nginx.conf
      - /etc/letsencrypt:/etc/letsencrypt
    command: "/bin/sh -c 'while :; do sleep 6h & wait $${!}; nginx -s reload; done & nginx -g \"daemon off;\"'"

  certbot:
    image: certbot/certbot
    restart: unless-stopped
    volumes:
      - /var/www:/var/www
      - /etc/letsencrypt:/etc/letsencrypt
    entrypoint: "/bin/sh -c 'trap exit TERM; while :; do certbot renew --webroot -w /var/www/certbot; sleep 12h & wait $${1}; done;'"

Nginx must be configured to publish the certbots well-known sites for the handshake and your sites must be configured to use the certificates from letsencrypt.

    server {
        listen 80;
        server_name <your-domain-name>;
        server_tokens off;
        location /.well-known/acme-challenge/ {
            root /var/www/certbot;
        }

        location / {
            return 301 https://$host$request_uri;
        }
    }

    server {
        listen 443 ssl;
        server_name vcm.winccoa.at;

        ssl_certificate     /etc/letsencrypt/live/<your-domain-name>/fullchain.pem;
        ssl_certificate_key /etc/letsencrypt/live/<your-domain-name>/privkey.pem;

        root /var/www;
        index index.html;

        location / {
            try_files $uri $uri/ =404;
        }