Beginning her film in the 1990s, Timoner has built a reputation in the documentary world, becoming the only two-time recipient of Sundance’s Grand Jury Prize for documentaries (DIG! and We Live In Public) these two works are in the permanent collection of New York's Museum of Modern Art.

In 2003, Timoner had a son, Joaquim, with Cinematographer Vasco Lucas Nunes. Vasco Lucas Nunes died in a motorcycle accident in March 2016.

The film won the Grand Jury Prize 2004 at the Sundance Film Festival, is now part of the permanent collection of the Museum of Modern Art in New York City, and was screened as finale of the Film Society of Lincoln Center and MoMA's 38th annual New Directors/New Films Festival, at MoMA in 2009.

Timoner also directed the socio-political feature documentaries, Join Us (2007), about the religious cult epidemic in America, using the Example of the Mountain Rock Church in South Carolina, and The Nature of the Beast (1994), a look at the U.S. prison system, and co-directed the short film Recycle, which premiered at Sundance in 2005, and screened at Cannes and in schools worldwide. In 2010, Timoner premiered her fifth feature-length documentary on climate change, Cool It at the Toronto International Film Festival in September 2010, and released it theatrically on November 12 that year through Roadside Attractions. In addition to documentaries, Timoner has made music videos for The Dandy Warhols, The Vines, Paul Westerberg, Lucinda Williams, Vanessa Carlton, The Jonas Brothers, and Run DMC, among others. She hosts a weekly talk show, BYOD, on Thelip.tv, featuring interviews with top film makers from the documentary world.

Timoner debuted We Live in Public at the Sundance Film Festival in 2009. The film considers some of the darker effects of modern media and Technology on personal identity through an examination of "the greatest internet pioneer you've never heard of", Josh Harris. The dot-com millionaire was referred to by reviewer Laurie Heuston as "a '90s dot-com millionaire who created fascist-themed, social experiments," endeavors that led eventually led to Harris' mental breakdown and financial downfall.

Timoner founded and is currently directing and producing what has been described as "a portal of cyber-series that take the users on the ride alongside the visionary risk-takers of today– those crazy enough to defy all limits to turn their big ideas into reality," the web channel called A Total Disruption. An interactive video network for innovators and entrepreneurs, she describes it as a "constantly releasing documentary". The channel documents the thought Leaders and innovators from companies like Twitter, Reddit, and BitTorrent who are using Technology to empower and educate; as of April 2013, Timoner edited 50 episodes for seven different web series, based on interviews with approximately 100 subjects (having shot 300 hours of film footage). The seed funds for the project were recently raised on Kickstarter, and yielded about 150% of their $96,000 goal.

Timoner's narrative film debut—a biopic on Photographer Robert Mapplethorpe entitled Mapplethorpe—received a grant through the Tribeca Film Institute’s 9th annual All Access Program. In 2013, Timoner initiated what has been termed a "constantly releasing documentary" via the web-channel called A Total Disruption, a platform presenting cyber-series about cutting-edge innovators who use Technology to "disrupt outdated industries, empower people, and change the world".

In 2015, Timoner's film BRAND: A Second Coming was chosen to be the opening night film at the 2015 SXSW Film Festival in Austin, Texas.