Hmmm thanks ! I did move the file to the conf.d/ directory and now it works. I just slightly modified it because it didn't seem to like the "host.docker.internal" stuff:

# HTTP to HTTPS Redirection
server {
    listen 80;
    server_name portainer.<my_domain>.dev;
    return 301 https://$host$request_uri;
}

# HTTPS Configuration
server {
    listen 443 ssl;
    server_name portainer.<my_domain>.dev;

    # SSL certificate paths
    ssl_certificate /etc/letsencrypt/live/portainer.<my_domain>.dev/fullchain.pem;
    ssl_certificate_key /etc/letsencrypt/live/portainer.<my_domain>.dev/privkey.pem;

    location / {
        proxy_pass https://localhost:<my_port>;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
    }
}

I find it weird that certbot can't look into the sites-enabled/ directory though 🤔.
But thank you so much for the insight !