The article highlights the obtained results on conducting an institutional audit of the professional military education system in educational institutions of the Ministry of Defence and the Armed Forces of Ukraine. The directions of further development of institutional audit mechanisms for evaluation of professional military education quality on the way to achieving compatibility of training processes according to NATO standards were substantiated. The results of the experiment confirm that institutional audit is a common element on the way to achieve compatibility of personnel training processes on NATO quality principles. The authors of the article use a system of general scientific and special methods of theoretical and empirical research (systematization, generalization, systematic approach) and methods of expert evaluation.