Renew Let's encrypt cert issued with cert-bot behind Cloudflare?

Hello,
I have several different websites with let’s encrypt certificates all running behind Cloudflare.

My servers are running Ubuntu 16.04lts with apache. Let’s encrypt certificates are installed with cert-bot.

The problem is that every time I need to issue a new certificate or to renew existing certificate I should pause Cloudflare so that the verification procedure may complete. This way I am unable to auto-renew my certificates using cron-job (as suggested in cert-bot documentation).

I’ve read through several “how-to” articles over the internet to fix this problem, with no luck…

So, my question is how can I achieve auto-renew without pausing Cloudflare?