- Praying with Our Hands: 21 Practices of Embodied Prayer from the World's Spiritual Traditions (2000)
- The St. Francis Prayer Book: A Guide to Deepen Your Spiritual Life (2004)
- The St. Clare Prayer Book: Listening for God's Leading (2007)
- Born Again and Again: Surprising Gifts of a Fundamentalist Childhood (2005)
- Strange Heaven: The Virgin Mary as Woman, Mother, Disciple, and Advocate (2006)
- The Lure of Saints: A Protestant Experience of Catholic Tradition (2006)
- Light in the Dark Ages: The Friendship of Francis and Clare of Assisi (2007)
- Almost Catholic: An Appreciation of the History, Practice, and Mystery of Ancient Faith (2008)
- Cloister Talks: Learning from My Friends the Monks (2009)
- Ralph Waldo Emerson: Essential Spiritual Writings, editor (2016)
- Meister Eckhart's Book of the Heart: Meditations for the Restless Soul (with Mark S. Burrows) (2017)
- The Pope's Cat (2018)
- Margaret's First Holy Week (2019)
- Meister Eckhart's Book of Secrets: Meditations on Letting Go and Finding True Freedom (with Mark S. Burrows) (2019)
- St. Francis of Assisi: His Life, Teachings, and Practice (2019)
- Margaret's Night in St. Peter's: A Christmas Story (2018)
- Lord, Make Me an Instrument of Your Peace: The Complete Prayers, St. Francis, St. Clare and other early Franciscans (2020)
- Feed the Wolf: Befriending Our Fears in the Way of Saint Francis (2021)
- Awake and Alive: Thomas Merton According to His Novices (2022)
- Sit in the Sun: And Other Lessons in the Spiritual Wisdom of Cats (2023)
- Meister Eckhart's Book of Darkness & Light: Meditations on the Path of the Wayless Way (with Mark S. Burrows) (2023)
