Mastroianni earned a César Award nomination for her first feature film appearance in André Téchiné's My Favorite Season (1993), starring her mother in the lead role.

Her first starring role came in 1995, opposite Melvil Poupaud in Le Journal du séducteur, a romantic comedy inspired by "The Seducer's Diary" chapter from Søren Kierkegaard's Either/Or.

She worked with Poupaud again in Three Lives and Only One Death (1996), playing the daughter of her real-life father, and in Time Regained (1999), also starring her mother.

Along with a few supporting performances in French films, she appeared in Gregg Araki's Nowhere (1997) and took time off to have her first child with sculptor Pierre Thoretton.

After appearances in Mike Figgis's Hotel (2001) and Le parole di mio padre (2001), she played the lead in Delphine Gleize's interconnected drama Carnages (2002), a winner at several international film festivals.

In July 2016, Mastroianni was named a member of the main competition jury for the 73rd Venice International Film Festival.

Other notable films in which Mastroianni has acted opposite Deneuve include Persepolis, A Christmas Tale, Three Hearts and Claire Darling.