Military personnel need physical fitness to effectively carry out operational military activities within their specific field of operation. This research investigates the effects of a 34-week training program on Angolan cadets’ body composition, muscle strength, and cardiorespiratory fitness. Seventy-four volunteer recruits, aged 18 to 26 years, were monitored during their eight-month military service, following an exercise program protocol comprising 12 weeks of strength training followed by 24 weeks of endurance training. Anthropometric variables, including body mass, body mass index, and fat mass, were assessed, along with cardiorespiratory fitness (VO2max), sprint performance, countermovement jump (CMJ), medicine ball throw, push-ups, and curl-ups. The physical training protocol encompassed running sessions, strength exercises, agility drills, and flexibility exercises. The initial assessment revealed gender differences in various parameters such as body mass, body fat percentage, VO2max, sprinting, countermovement jump (CMJ), medicine ball throw, and push-ups. Following the training program, changes were observed in all variables (effect size between 0.48 and 2.33, p < 0.01) for the participants. Significant interactions (sex × time) were found in body mass (F = 5.18, p = 0.03, ηp2 = 0.06), body fat percentage (F = 5.31, p < 0.01, ηp2 = 0.14), and medicine ball throw (F = 10.84, p < 0.01, ηp2 = 0.13). Specifically, males exhibited a greater reduction in body mass (females: 2.70%, males: 3.47%, p < 0.05) and a substantial improvement in ball throwing performance (females: 7.74%, males: 11.47%, p < 0.01), while females experienced a greater reduction in fat mass (females: 5.34%, males: 3.15%, p < 0.01). The physical training regimen effectively influenced body composition, particularly in enhancing strength performance among males. The integration of exercise programs with military service led to a notable reduction in fat tissue and an increase in lean tissue. Hence, the development of tailored training protocols is imperative to enhance the physical capacity and overall health of military recruits, considering sex-specific characteristics and physical attributes.