Decker produced and directed her first short film, Naked Princeton, in 2005.
In 2008, Decker co-directed the documentary Bi the Way with Brittany Blockman, which focused on bisexuality in the United States. Despite being described by Variety's Joe Leydon as a "once-over-lightly examination of an alleged cultural phenomenon", the film nevertheless went on to win the Alternative Spirit Grand Prize at the Rhode Island International Film Festival.
Decker wrote and directed her second short film, Where Are You Going, Elena?, in 2009. In 2012, Decker wrote and directed the short film Me the Terrible, which was praised by Richard Brody of The New Yorker as a "wondrous short film."
In 2013, Decker wrote, produced, and directed her first feature film, the experimental psychological thriller Butter on the Latch. The film garnered praise from Eric Kohn of Indiewire, who said Decker's career is "one to keep an eye on", and Peter Debruge of Variety, who noted that "... Decker has fashioned the kind of feature debut the film industry simply doesn’t support, but would do well to encourage: a visually poetic, virtually free-form groove in which emotion, rather than narrative, guides viewers through a young woman’s visit to a Balkan folk music camp."
In early 2014, she completed her second theatrical film, the experimental erotic thriller Thou Wast Mild and Lovely, starring Sophie Traub and Decker's frequent collaborator Joe Swanberg. To raise money for the film's post-production, Decker ran a crowdfunding campaign on the website Kickstarter with a goal of $15,500. The campaign closed on August 22, 2013, having successfully raised $18,517. In his review of the film, Eric Kohn of Indiewire gave the film a positive B+ rating and commented, "Its labyrinthine characteristics suggest the unholy marriage of Ingmar Bergman and David Lynch. While nowhere near the same level of refinement as those giants, Decker concocts a wholly enveloping vision of isolation told with a grimly poetic style that wanders all over the place but never stops playing by its own eerie rulebook."
In September, 2014, it was announced that Butter on the Latch and Thou Wast Mild and Lovely had been picked up for a theatrical and VOD distribution by Cinelicious Pics with a planned release set for November, 2014.
Decker has also appeared as an actor in many independent films, including Joe Swanberg's Uncle Kent, Onur Tukel's Richard's Wedding, Saturday Morning Mystery, the romantic tragedy Loves Her Gun, and Stephen Cone's critically lauded drama film Black Box in 2013.
In November 2015 Decker served on the Jury of the 33rd Torino Film Festival. The Italian festival had already paid tribute to her work in the Onde section of 2014 edition.