Baker's first feature film was Four Letter Words, a film revolving around the looks, views, attitudes and language of young men in America. Baker wrote, directed and edited the film. Baker then went on to make Take Out, which he co-wrote, co-directed, co-edited and co-produced with Shih-Ching Tsou. The film revolves around an illegal Chinese immigrant falling behind on payments on a smuggling debt, leaving him only one day to come up with the money. The film had its world premiere at the Slamdance Film Festival on January 18, 2004, but was not given a limited release until June 6, 2008. Baker's third feature film Prince of Broadway premiered at the Los Angeles Film Festival on June 22, 2008. The film follows a New York street hustler who makes his living creating name-brand knock offs, and his discovery that he has a son. Baker directed, wrote, co-produced, shot and edited the film, which was given a limited release on September 3, 2010.

Baker is also one of the original creators of the sitcom Greg the Bunny, starring Seth Green and Eugene Levy. The show is based on a series of short segments that Baker directed and wrote, which aired on the Independent Film Channel and which were in turn based on a public-access television show called Junktape. In 2010, Baker, Spencer Chinoy and Dan Milano created a spin-off called Warren the Ape; the series aired on MTV and was canceled after one season.

Baker's fourth feature, Starlet, was co-written with Chris Bergoch and stars Dree Hemingway and Besedka Johnson. Starlet explores the unlikely friendship between 21-year-old Jane (Hemingway) and 85-year-old Sadie (Johnson), two women whose lives intersect in California's San Fernando Valley. The film had its world premiere at SXSW on March 11, 2012, and was given a limited release on November 9, 2012. It opened to mainly positive reviews and holds an 88 percent rating on Rotten Tomatoes. Baker's fifth feature, Tangerine, follows a transgender sex worker who discovers her boyfriend and pimp has been cheating on her. The film was shot using three iPhone 5s smartphones and received praise for its groundbreaking filmmaking techniques. Tangerine features Kitana Kiki Rodriguez, Mya Taylor, Karren Karagulian, Mickey O'Hagan and James Ransone and was executive produced by Mark Duplass, and Jay Duplass. Baker again co-wrote the script with Bergoch; he also co-produced, co-shot and edited the film. It had its world premiere at the 2015 Sundance Film Festival on January 23, 2015, and was given a limited release on July 10, 2015. It received extremely positive reviews, and currently holds a 97 percent rating on Rotten Tomatoes.

Baker's most recent feature, The Florida Project, premiered in the Directors' Fortnight section of the 2017 Cannes Film Festival, and was theatrically released in the United States on October 6, 2017, by A24. Once again, Baker edited the film himself and co-wrote the script with his frequent collaborator Chris Bergoch. The plot follows a six-year-old girl living in a motel with her rebellious mother in Greater Orlando as they try to stay out of trouble and make ends meet. The film was praised for its performances (particularly that of Willem Dafoe as the motel manager) and Baker's direction, and was chosen by both the National Board of Review and the American Film Institute as one of the top 10 films of the year. Dafoe earned Best Supporting Actor nominations at the Oscars, Golden Globes and BAFTA Awards.