In 2014, Stoll also played Austin Reilly, an NYPD police officer, in the action film Non-Stop, and Paul Altman in the comedy-drama This Is Where I Leave You. In 2015, Stoll played Ben Day in the film Dark Places, based on the novel by Gillian Flynn, and had a major role as the villain in the superhero film Ant-Man, playing Darren Cross, later reimagined as the supervillain Yellowjacket. The following year, he reunited with Woody Allen, playing gangster Ben Dorfman in his 2016 film Café Society. Also in the summer of 2016, he played the wily Greek warrior Ulysses in the Public Theater production of Troilus and Cressida by William Shakespeare, in Central Park.
Stoll became engaged to his girlfriend Nadia Bowers, an actress and descendant of Maximilian de Beauharnais and Joséphine de Beauharnais, in October 2014. They were married on June 21, 2015. They welcomed their first child in October 2015.