The aim of this study was to analyze the morphological and functional changes in military recruits after twelve weeks of physical training. The sample consisted of 130 volunteer recruits aged 18-19 years. Anthropometric variables were assessed (body weight, height, body mass index, arm, waist, and hip circumference, waist/hip ratio, skinfold thickness of the triceps, suprailiac, and abdomen, and body fat percentage) and the sit-up test (1 minute), push-up test, and 12-minute running test. The physical training protocol involved running workouts, strength, agility, and flexibility. Descriptive statistical procedures were performed with mean, standard deviation, variance, and percentage and the comparison between the two moments was performed using the Student t test for dependent samples. The significance level was set at p <0.05. The results demonstrated a decrease in the sum of the three skinfolds (42.7±25.2mm to 33.9±17.7mm), a decrease in fat percentage (14.1±7.3% to 11.8±6.1%), an increase in lean mass (57.6±6.0kg to 58.6±8.0kg), and decreased fat mass (10.1±6.4kg to 8.3±5.2kg). They also showed improvements in push-up test (21.3±9.0 to 33.5±8.9), sit-up test (35.2±8.3 to 49.8±7.4), the 12 minute test (2212±316m to 2760±214m), and V̇O2max (35.2±8.3ml.kg-1.min-1 to 49.8±7.4 ml.kg-1.min-1). No differences were observed in body mass, height, body mass index, or hip circumference. According to the above, it was found that the methodology adopted in the physical training was effective in reducing the percentage of fat and increasing cardiorespiratory fitness, improving the physical capacity and health of the military recruits.