- Quantum Theology: Spiritual Implications of the New Physics (1997)
- Reclaiming Spirituality (1998)
- Poverty, Celibacy, and Obedience: A Radical Option for Life (1999)
- Religion in Exile: A Spiritual Homecoming (2000)
- Evolutionary Faith: Rediscovering God in our Great Story (2002)
- Catching Up with Jesus: A Gospel Story for Our Time (2005)
- The Transformation of Desire: How Desire Became Corrupted and How We Can Reclaim It( 2007)
- In the Beginning Was the Spirit: Science, Religion, and Indigenous Spirituality (2012)
- God in the Midst of Change: Wisdom for Confusing Times (2013)
- The Meaning and Practice of Faith (2014)