The couple have recently appeared to be on steady ground following the revelation that Janine (Charlie Brooks) is pregnant with Michael's child.
However, speaking to Inside Soap, Shepherd warned that viewers have not yet seen the last of trouble between the pair.
"The relationship is going to get very fraught and rocky - mountainous, actually," the actor explained. "I gather that Janine has made a habit of killing off her husbands, so Michael will have to keep one eye open where she's concerned!"
Discussing the connection between the duo, he continued: "They both have this 'black dog' that follows them around - it's a darkness. They share similar histories with family dysfunction, so he knows why Janine is so unpredictable and uneven. He sees himself in Janine."
Shepherd also joked about how Michael and Janine's child might cope with having such twisted parents.
He said: "I pity Michael and Janine's baby! How would I rate his skills as a father? Quite low. Imagine Michael changing a nappy! But he sees this as a chance to redeem himself."
> EastEnders' Michael will clash with Derek, says Steve John Shepherd
> Read more EastEnders spoilers and news
Watch Michael's EastEnders character trail below: