Her directorial debut was the groundbreaking film Go Fish (1994), a lesbian love story. Made on a shoestring budget, it was one of the truly "independent" films of the mid 90s, and certainly one of the first in the lesbian genre. It premiered at the Sundance Film Festival in 1994. The film was co-written and co-produced with Guinevere Turner, who was Troche's girlfriend at the time. Her next feature film was Bedrooms and Hallways (1998) which explored male sexuality. She also directed The Safety of Objects (2001), which was adapted from the short stories of A. M. Homes and focused on heterosexual love in suburbia.

Her television work is just as extensive as her film work. She directed an episode of the HBO hit drama Six Feet Under. And for three seasons, she has been a director and writer for the Showtime series The L Word, the groundbreaking show about lesbian friends living in LA. She has served as the associate producer for the series and was recently promoted to co-executive producer. She has also expanded her writing and directing credits, writing an episode for the series South of Nowhere and directing an episode of the series Touching Evil, as well as Ugly Betty and Law & Order.