MZA was formed in 1991 to meet a need for advanced simulation and analysis of adaptive optics systems at what is now the Air Force Research Laboratory (AFRL). MZA was founded by four researchers having historical links to common projects: Bob Praus, president and software engineer, Steve Coy, a physicist and software designer, and two others who have since left. In December of 1992 MZA was awarded the Phillips Laboratory, four-year, three-million dollar ATP Modeling and Simulation Support (AMASS) contract. The company has been growing and thriving since. Steve Coy left the company in June 2011. In 2012, MZA ownership of the company was spread to employees through the establishment of an Employee Stock Ownership Plan (ESOP).

For 17 years consecutively, since 2001, MZA has been named to the New Mexico Technology Flying 40 , a group of New Mexico technology businesses recognized for their rapid growth.