His most recent book Keeping Faith: A Skeptic's Journey draws on time spent living as a member of the monastic communities of the Trappist Abbey of Gethsemani in Kentucky and the San Francisco Zen Center as a means to examining what it means to a skeptic to have and keep faith. Keeping Faith weaves frank conversations with Trappist and Buddhist monks with a history of the contemplative life and meditations from Johnson’s experience of the virtue we call faith. It received the 2004 Kentucky Literary Award for Nonfiction and the 2004 Lambda Literary Award for best GLBT creative nonfiction.

Johnson has served as a contributor to Harper's Magazine, the New York Times Magazine, and many literary quarterlies, and has received numerous literary awards, among them a James Michener Fellowship from the Iowa Writers Workshop and National Endowment for the Arts Fellowships in both fiction and creative nonfiction. His writing also received a Northern California Book Reviewers nomination for best fiction (for Scissors, Paper, Rock, Washington Square Press) and the American Library Association's Stonewall Book Award and Lambda Literary Awards for best creative nonfiction (for Geography of the Heart, Scribner). He contributes occasional commentaries to National Public Radio and has written the narration for several award-winning public television documentaries and personal films. He serves on the faculty of the creative writing program at the University of Arizona and is currently completing The Man Who Loved Birds: A Novel and is a 2007 John Simon Guggenheim Fellow.

He has received awards from the Wallace Stegner and James Michener Fellowships in Fiction and National Endowment for the Arts Fellowships in both fiction and creative nonfiction. He has also received a Kentucky Literary Award, two Lambda Literary Awards for best creative nonfiction, as well as the American Library Association's Stonewall Book Award for best gay/lesbian nonfiction. He received a 2007 fellowship from the John Simon Guggenheim Foundation to support completion of his third novel and to begin research and writing on a nonfiction project.

Novels

• Crossing the River, Birch Lane Press
• Scissors, Paper, Rock, Washington Square Press

Memoir

• Geography of the Heart: A Memoir, Scribner's.