The 18-year-old, who made four senior appearances for City last term, will spend the upcoming campaign in France's Ligue 1 with Lille.
"I feel very happy to have signed because it is a new step in my career and it is a good opportunity for me to develop as a player. I hope to get much stronger next season, and I'm really looking forward to getting started," he told City's official website.
"It is very important for me to play in a professional league for the first time, and it is important for me to experience what it is like to play in that environment. It is very different to what I have played in before, but I watched some of the games last year and I think it will be a good league for my development."
Meanwhile, City's development side manager Patrick Vieira added: "Marcos is joining a league that is very demanding physically, but is very good at developing young players. It is great that he has the chance to take his next step in a very strong league that will be challenging for him."
Lopes joined City as a trainee from Benfica in 2011.