The MAAF was founded with a simple email discussion group in February 1998 by Kathleen Johnson when she was an active duty Sergeant First Class with the Army's Criminal Investigative Division (CID).

The group's early efforts included letter writing campaigns reminding public figures such as Tom Brokaw not to use the phrase, "There are no atheists in foxholes."

Other efforts supported active duty military personnel seeking to include, "Atheist" or, "Agnostic" on their dog-tags instead of the more common, "No Rel Pref" which meant the individual had no religious preference.

[4] While the BSA claims to be a private organization with a legal right to discriminate, the MAAF calls for an end to federal support in the form of funding and free access to military bases.

[7][8] Although no major changes were made as a result of the complaints, the Army did remove a section from the Spiritual Fitness website which equated the military flag folding tradition with Christian religious tenets.

In July, 2012 the MAAF published demographics from the United States Department of Defense that confirmed that atheists and agnostics in military ranks far outnumber several other groups, such as Hindus, Jews, Muslims, and Buddhists yet have no representation in the chaplain corps.

This same study also showed that Evangelical Christians make up an inordinately large proportion of the chaplain corps when compared to the relatively small percentage of military members who hold such beliefs.

[12] In July 2007, Major Freddy Welborn[13][14] attended a meeting of atheist service members in Iraq under the umbrella of the MAAF and organized by Army Specialist Jeremy Hall.

Active duty Army Sergeant Justin Griffith sought to hold a similar event called Rock Beyond Belief but was initially refused the same level of support.

A set of three, 13 foot (4 meter), wooden crosses erected by a small group of Marines in 2003 had stood without controversy until a news story caught the attention of the MAAF.