Marcotte is resigning so that he can take care of his son-in-law, who he says is gravely ill, a city hall spokesperson said.
Marcotte was arrested in April and charged with fraud, corruption, breach of trust and conspiracy by Quebec's anti-corruption task force. But he has refused to quit as mayor. Mascouche residents and councillors had been pressuring him to resign for months.
Municipal Affairs Minister Sylvain Gaudreault welcomed the mayor's decision. He empathized with the Mascouche population and said that citizens have been waiting a long time for Marcotte's resignation.
Stéphane Handfield, the spokesperson for Mascouche's opposition party, said that residents can finally "turn the page."
Handfield said that it's possible that an anti-corruption bill recently tabled by the Parti Québécois could have influenced Marcotte's decision.
The bill would allow a judge to order any member of council, including the mayor, to be suspended with pay if they face a criminal charge that could lead to a sentence in a federal prison.
Earlier this month, Marcotte said he was taking time off to reflect, but that he would not resign.
Over the summer, city council meetings turned chaotic as residents called for the mayor's resignation. Marcotte was escorted to and from the meetings by a corps of local police, at a cost of more than $5,000 per meeting.
In August, the municipality was forced to shut down a council meeting when about 100 residents drowned out the mayor with jeers.
City councillors in Mascouche have also pleaded with Quebec's minister of municipal affairs to help them get rid of their mayor. But last month, the Quebec government said it would not put the city under trusteeship.
The charges against Marcotte stem from the provincial anti-corruption task force's investigations into allegations of conflict of interest and other irregularities in the awarding of municipal contracts.
Former MNA will run for mayor's job
Allegations against Marcotte suggest that a company called Mascouche Transport and Excavation — which received contracts from the city worth nearly $40 million in 2008 and 2009 — did millions of dollars in free work on Marcotte's home.
The company had financial backing from construction entrepreneur Tony Accurso, who is charged with 12 counts of fraud, forgery, conspiracy, breach of trust and municipal corruption.
None of the accusations have been proven in court.
In November, former MNA Guillaume Tremblay announced he would run for mayor of Mascouche, despite the fact Marcotte had not yet resigned his post.
Tremblay was a Parti Québecois MNA in the riding of Masson for the last four years. Before getting involved in provincial politics, Tremblay sat as an Independent city councillor for Mascouche.
The 28-year-old said he will run for mayor under the banner of the official opposition party, Vision Démocratique de Mascouche.