The short won a prize at the 2004 Sundance Film Festival and Boden and Fleck were subsequently invited to the Sundance Writer's Lab to receive professional feedback on the Half Nelson screenplay. The film did not receive adequate financing for years, and while trying to initiate the project, Fleck explains: "We were trying to get it off the ground so we had plenty of time to keep writing and rewriting. I think the time was valuable because I think we made it as good as we could."
Boden and Fleck have since co-written and co-directed the 2008 film Sugar, which premiered at the 2008 Sundance Film Festival, about a 19-year-old Dominican who immigrates to the United States to play minor league baseball. The two wrote the screenplay after researching about many Dominican immigrants who arrive in America to play in minor league towns, saying: "The stories we heard were so fascinating that it became what we were writing before we'd even decided it was our next project". They also collaborated on a screen adaptation of Ned Vizzini's young adult novel It's Kind of a Funny Story, which was released on October 8, 2010.
In 2012, the duo began work on a gambling movie called Mississippi Grind. The idea for the film came when they would visit riverboat casinos in Iowa. By this point in their career, Boden and Fleck had fully committed to each other, "In the early days of our partnership we had to navigate a lot of issues concerning trust and ego. Nowadays, those issues are almost entirely gone. Having a creative partner who you can wholly trust is a wonderful asset."
In April 2017, Boden and Fleck were hired to direct the upcoming Marvel Studios film Captain Marvel.
