The Estonian Defense Forces are the basis of military service, mandatory for all male citizens of the Republic of Estonia who are at least 17 years old. The physical load in military service, especially in the first stage, is significantly greater than for men in everyday life. Therefore, it is important to know if health promotion in civilian life adequately prepares young people for military service and to what extent pre-military health behaviors affect physical performance during service. The purpose of this work was to examine conscripts' physical fitness at different stages of military service and its relationships with previous lifestyle. Soldiers' physical fitness was estimated three times during military service using three tests: sit-ups, push-ups and 2-mile run. Lifestyle and socio-economic background data was collected by a web-based questionnaire (n = 235). Linear regression analysis was performed using Army Physical Fitness Test (APFT) scores as dependent variables and questionnaire data as independent variables. The socio-economic background variables had no effect on physical fitness scores throughout the training period (p > 0.05). Young men that were physically more active daily, did sports, had healthier diet and did not smoke before entering military service showed better physical fitness test results throughout the period of service (p < 0.05). The effect of participation in sports was evident, as the conscripts with previous sports experiences demonstrated higher fitness tests scores (p < 0.01). These findings show that health promotion initiatives or programs for promoting physical activity and healthy diet, and preventing obesity and tobacco use, can also have a positive effect on the physical performance of young men during military service.