Johnson devoted much of his work to church growth and spiritual formation. Through the Institute of Church Renewal he developed a number of programs and resources for congregations aimed to promote growth and vitality. He furthered this work through founding the Columbia Theological Seminary Press, enabling the publishing of many book and articles intended to educate all church leaders. Seeing church growth as more than simply evangelism, he created and began the Doctor of Ministry in Christian Spirituality at Columbia Theological Seminary, which focuses on "congregational leadership while exploring God's relationship to persons, the community of faith, and the world, including the ethical and social dimensions of spirituality." He also began the Certificate in Spiritual Formation extending the education of spiritual development to all people so to encourage church growth in a variety of ways. This program allows "people in the pulpit, in the pew, in all denominations and stages of life to explore the community-grounded Christian spirituality that is rooted in scripture, theology, a history of the tradition, reading in the spiritual classics, prayer and meditation, and in skills for assisting others on a spiritual journey." Both of these are still important programs that attract and teach church leaders from around the United States.
