Michel stepped down after he was pressured by the biggest party in his coalition--the New Flemish Alliance (N-VA)--to quit support for the UN migration pact, a cause celebre for European anti-immigration parties.
"I am taking the decision to offer my resignation. I am now going to see the king" to inform him, he told Belgian lawmakers Tuesday.
The resignation comes two days after demonstrations against the pact in central Brussels descended into scuffles, with police forced to use tear gas and water cannon to restore order.
The liberal premier, who took office in 2014, has steadfastly defended the Marrakech migration pact, saying it presented an "opportunity for better European and international cooperation."
All four parties in Belgium’s coalition initially supported the non-binding UN accord, which is meant to streamline and smooth international mass migration.
Nevertheless, the right-wing New Flemish Alliance (N-VA) changed its mind in late October and pulled out of the coalition the day before Michel flew to Morocco to sign the deal.
Critics said the N-VA's move was the opening shot in a campaign before federal elections in May.
This is not the first time Belgium has faced a constitutional crisis. In 2011, the country went for more than 500 days without a national government, owing to divisions between wealthier Dutch-speaking Flanders in the north and the run-down French-speaking former industrial heartland of Wallonia in the south.
Before this latest fallout, Michel had been able to hold together a delicate four-way coalition involving liberals, Flemish Christian Democrats and the nationalist N-VA, which eventually wants a separate homeland in Flanders.
Belgian media said the king would meet party leaders Wednesday before deciding whether to accept his premier's resignation.