When running Let's Encrypt with nginx, if we get the error 404 at .well-known/acme-challenge try running it using the command below with nginx stopped.

systemctl stop nginx
certbot certonly --standalone -d example.com --non-interactive --agree-tos --email support@example.com
systemctl start nginx

This should pass the verification step which otherwise will error with 404 issue.

Update nginx conf.d configuration to have the below lines.

server {
    index index.html index.htm;
    server_name example.com;
    
    # ..
    
    listen [::]:443 ssl ipv6only=on; # managed by Certbot
    listen 443 ssl; # managed by Certbot
    ssl_certificate /etc/letsencrypt/live/example.com/fullchain.pem; # managed by Certbot
    ssl_certificate_key /etc/letsencrypt/live/example.com/privkey.pem; # managed by Certbot
    include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
    ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot
}

server {
    if ($host = example.com) {
        return 301 https://$host$request_uri;
    } # managed by Certbot


    listen 80 default_server;
    listen [::]:80 default_server;
    server_name example.com;
    return 404; # managed by Certbot
}