You must clean the poop as soon as he is done... many dogs eat their own poop as gross as it is, because to them it doesn't smell like poop, it smells like the same food they ate. Mine used to do it, I clean after the poop as soon as he is done, but also taught him "no" don't eat it.
Do keep in mind though, that sometimes, they will eat it because they are not getting enough nutrients.
My advice - as soon as it goes out, clean it up.