Independent film route and move into producing (2013–present)

Biel starred in the thriller film Emanuel and the Truth About Fishes, which premiered at the Sundance Film Festival on January 18, 2013. In April 2008, Biel began working on the political satire Nailed, with Jake Gyllenhaal. The film centers around a woman who accidentally gets a nail lodged in her head and travels to Washington, D.C. to fight for better health care. In May 2009, Biel spoke about the film's production turmoil, saying: "That was definitely an experience, something I could not say no to. I am a huge David O. Russell fan. It's just heartbreaking that so many people put so much work into this particular project only to have it sit there, unfinished." The film was released on video on demand on February 10, 2015, and received largely negative reviews from critics.

In 2015, Biel starred in the independent drama Bleeding Heart, in which she plays a yoga instructor named May who meets her biological sister Shiva (Zosia Mamet), a sex worker, for the first time. The film premiered on April 17, 2015, at the Tribeca Film Festival, receiving mixed reviews, though Biel earned praise for her performance. Richard Lawson of Vanity Fair commented: "Though she's not given too much to work with in terms of character, Biel plays May with appealing nuance, creating a low-key, bliss-based Angeleno, all light and airy and gentle and poised, who discovers within herself an untapped hardness and anger and strength... when Biel has to conjure up more profound emotions, she proves adept, and surprisingly subtle." Clayton Davis of AwardsCircuit.com also praised her performance, writing, "With an internalized and very subtle performance, Biel excels in her ability to find the very motivation of May."

In 2016, Biel co-starred with Patrick Wilson (with whom she had worked on The A-Team) in the thriller A Kind of Murder, based on the novel The Blunderer by Patricia Highsmith. She voiced the character Vix in the animated film Spark, with Susan Sarandon and Hilary Swank, which was released in 2016. Biel also appeared in the drama The Book of Love, based on the book The Devil and the Deep Blue Sea, about an introverted architect (Jason Sudeikis) who loses his wife (Biel) and sets out to help a teenager named Millie (Maisie Williams). Biel also produced the project from its conception some years prior, and was directed by Bill Purple, who directed her in the short film Hole in the Paper Sky. The film was released in January 2017.

On August 2, 2017, Biel's eight-episode limited series murder mystery, The Sinner, debuted on USA Network. Biel is both executive producer and played the series' lead character Cora Tannetti. She stated that she moved into production so that she could develop projects with challenging and interesting roles rather than waiting for them to happen.

In October 2021, it was announced Biel would star and executive produce the true-crime drama Candy for Hulu.

Biel at the 81st Academy Awards in 2009