Due to their specific mode of operation, military personnel are challenged physically as well as mentally. In most countries, the use of food supplements by military personnel is not regulated, and a high prevalence of supplementation is expected. However, data on this are scarce or very limited, without insights into the importance of supplementation for the intake of bioactive substances. Our goal was, therefore, to develop a study protocol to enable an assessment of the prevalence of using food supplements and an estimate of the contribution of supplementation practices to the dietary intake of specific nutrients and other compounds. The protocol was tested in a study of Slovene Armed Forces (SAF) personnel. Data were collected using an anonymous questionnaire in a sample of 470 participants from different military units—about half from the barracks located across the country, and the other half returning from military operations abroad. To provide meaningful results, we recorded the use of food supplements and functional foods available in single-sized portions (i.e., energy drinks, protein bars, etc.). Altogether, 68% of the participants reported supplementation, most commonly with vitamin, mineral, and protein supplements. Military rank, participation status in military operations, and physical activity were the main determinants of the specific supplements used. Surprisingly, a lower prevalence of overall and protein supplementation was observed in subjects returning from military operations abroad (62 vs. 74%) than in personnel stationed in barracks across Slovenia; however, the frequency of the use of energy drinks and caffeine supplements was higher in this population (25 vs. 11%). The study design allowed for estimations of the daily intake of supplemented bioactive compounds. We describe the challenges and approaches used in the study to support similar studies in the future and within other populations.