His books include Structure and Creativity in Religion: Hermeneutics in Mircea Eliade's Phenomenology and New Directions, Coming to Terms: Indochina, the United States, and the War, Comparative Philosophy and Religion in Times of Terror, and Gandhi after 9/11: Creative Nonviolence and Sustainability.

Allen has conducted research on various peace and justice topics, focusing on the philosophy of Mahatma Gandhi.

[6] His work on Gandhi's philosophy includes research on violence and nonviolence, war and peace, terrorism, truth, Vedanta, Hind Swaraj and the Bhagavad-Gita, marginality, technology, and economic and environmental sustainability.

He presented an alternative to anti-Gandhians, non-Gandhians, or reactionary Gandhians who over-idealized and decontextualize Gandhi and his philosophy.

According to Neelmani Jaysawal, "Gandhi’s philosophy has been presented in a number of contexts ranging from his ideas on religion, violence and satyagraha to his conception of a new society".

He highlighted various principles from Eliade's methodology and presented the relationship between the sacred and the profane, and the evaluation and choice implied in the dialectic.

[13] Allen authored a paper on Eliade's critique of contemporary Western philosophy and culture, and presented his analysis of engaged self-other Marxist, feminist, Hindu and Buddhist encounters.