Introduction: Optimal diet together with good physical fitness maintains readiness and military performance during longer deployments. The purpose of this study was to describe changes in dietary macronutrient and energy intake, total physical activity and body composition during a 6-month deployment in South Lebanon. Furthermore, associations of diet macronutrient intake and physical activity on body composition were also studied. - Materials and Methods: Forty male soldiers kept a 3-day food diary and their body composition was measured via bioimpedance and ultrasonography. Total physical activity was evaluated by accelerometers in a subgroup of participants. Measurements were conducted in the PRE-, MID-, and POST-deployment. - Results: Mean carbohydrate intakes were 39.5–42.6 E%, protein intakes 18.7–22.3 E%, and fat intakes 34.9–35.7 E%. Daily energy intake remained stable (10.1–10.3 MJ/D). Total physical activity was decreased during deployment (e.g., step count from 9,835 ± 2,743 to 8,388 ± 2,875 steps/day, p = 0.007). Skeletal muscle mass and subcutaneous fat increased by 1.3% (p = 0.019) and 1.9% (p = 0.006), respectively. Energy and fat intake associated positively with body mass and skeletal muscle mass (r = 0.31–0.48, p < 0.05–0.001). - Conclusions: Carbohydrate intakes and physical activity were low, compared with the general recommendations. Protein intakes were relatively high. Skeletal muscle mass and subcutaneous fat increased. Suboptimal diet together with low level of physical activity may have a negative impact on body composition, physical performance, and cardiometabolic health. Consequently, soldiers should be encouraged to consume more fiber-rich carbohydrates and less saturated fatty acids as well as maintain a high level of physical fitness to sustain military readiness during long-term deployments.