Originally from Edmonton, Alberta, Labonté studied English and political science at Carleton University in Ottawa, where he was an editor for The Charlatan. Following school he joined the Ottawa Citizen in 1972 as an editor, later writing film and book reviews, and was a contributor to The Body Politic. In 1980, he contributed to an Ottawa Citizen series on gay life in Ottawa, becoming one of the first Canadian journalists ever to come out in the pages of a mainstream newspaper.
During his time contributing to the Citizen, Labonté began a relationship with Norman Laurila, then an employee at Glad Day Bookshop in Toronto. The couple subsequently moved to Los Angeles, where they would become co-founders of the influential LGBT bookstore A Different Light. Although their relationship broke up in 1983, they both remained involved in the store, with Labonté managing the Silver Lake store and Laurila managing a new branch in New York City.
After Michael Thomas Ford stepped down as editor of Cleis Press's annual Best Gay Erotica series in 1996, Labonté was invited to become editor of the series, because the deadline for the next anthology was imminent and his job as a bookstore manager meant he would have extensive contacts in the gay literary world whose work he could call in quickly. He remains the editor of the series to this day, and has also edited numerous other themed anthologies for the company. He has also published several anthologies with the Canadian Arsenal Pulp Press, and has written book reviews for Books to Watch Out For/Gay Men's Edition, Book Marks, PlanetOut, Q Syndicate and Publishers Weekly.
He has won three Lambda Literary Awards for his work as an editor, for Best Gay Erotica 2005, First Person Queer (coedited with Lawrence Schimel) in 2008 and Best Gay Erotica 2009; his other titles have included The Future Is Queer, Second Person Queer and I Like It Like That: True Tales of Gay Desire.