Nouwen put his stamp on Christian spirituality by conveying his understanding of the belovedness of God, that we are the beloved sons and daughters of God. Books such as the Return of the Prodigal Son, Adam, Compassion and Life of the Beloved all emphasize this. One of his major ongoing themes involved his struggle reconciling his depression with his Christian faith.

In Return of the Prodigal Son, for example, Nouwen describes love and forgiveness as unconditional. Though this is not a novel idea, Nouwen's approach is arguably unique as he approached this theme from the angles of the younger son, the elder son, and the father. Each captures the unconditional quality of love and forgiveness in their own way. The younger son's life shows how the beloved lives a life of misery by thinking he can be loved only by meeting certain qualifications of the lover (which he fails to meet). The elder son's actions shows how the beloved can be depressed because he thinks he should receive greater love because he has done all the right things (i.e., that he has met these qualifications). The father alone understands how to love and forgive and is able to do so and be happy. Nouwen explains that we are the younger son at times (when we think we don't deserve the love or the forgiveness) and the elder son at times (when we think we deserve love or that another doesn't deserve it more than us), but that we are all called to be like the father (and that only by being like the father can we come closer to being loved as we should be loved).

Nouwen also wrote several essays on the necessity of peacemaking. He used God's Love as a justification for the preservation of life, as well as saying "No" to both Vietnam and Nuclear War.

Nouwen also wrote, in part, about his struggles reconciling his priestly vows of celibacy with his human desire for physical and emotional intimacy.

Henri Nouwen was strongly influenced by Thomas Merton. See "Encounters With Merton".

Nouwen struggled with his sexuality. "Although his sexuality was known by those close to him, he never publicly claimed a homosexual identity." Although he never directly addressed the matter of his sexuality in the writings he published during his lifetime, he acknowledged the struggle both in his private journals and in discussions with friends, both of which were extensively referenced by Michael Ford in the biography Wounded Prophet, which was published after Nouwen's death. Ford suggests that Nouwen only became fully comfortable with his sexual orientation in the last few years of his life, and that Nouwen's depression was caused in part by the conflict between his priestly vows of celibacy and the sense of loneliness and longing for intimacy that he experienced. Ford conjectured, "This took an enormous emotional, spiritual and physical toll on his life and may have contributed to his early death." There is no evidence that Nouwen ever broke his vow of celibacy.