His latest book is titled Getting Away with Murder: The Real Story Behind American Taliban John Walker Lindh and What the U.S. Government Had to Hide (2004).

Mahoney has also authored numerous articles and monographs on presidential history, foreign policy, international trade, and political risk; and a volume of poetry in Spanish, titled Pétalos (1995).

A member of the Democratic Party, Mahoney served as chief speechwriter in the presidential campaigns of Senators Gary Hart and Paul Simon in the 1980s.

The inauguration of Arizona's executive offices changed from March to January, which meant Mahoney served two fewer months when his term ended in 1995.

Mahoney served as head of the Baker Institute for Peace and Conflict Studies at Juniata College until his departure to the School of Public and International Affairs at North Carolina State University.