Body composition (BC) offers essential insights into the physical condition and performance capacity of athletes. Several factors can influence athletes' BC, such as nutrition, which can improve lean mass (LM) and body fat percentage (%BF). This longitudinal observational study aimed to investigate the factors influencing BC in professional female football players, including hormones, dietary habits, and physical activity, as these are relevant to their sport performance and health. Data related to dietary habits, DXA measurements, serum hormones, menstruation, and GPS metrics were collected in November 2023 and late March 2024 from 38 female football players from the Real Sociedad team. Of the 38 players enrolled, 35 completed all assessments and were included in the final analyses. Spearman correlations and linear regression analyses were performed. Statistically significant models were executed for %BF and LM (adjusted R2 = 0.55 and 0.47 respectively). For %BF, total testosterone had a positive influence while HSR (high-speed running) per minute, FSH, distance covered per minute, prolactin, and fat intake, influenced negatively. In the LM model, positive associations were total testosterone, progesterone, age, ACTH, and carbohydrate intake, while insulin, distance covered per minute, and, SHBG had negative associations. These results emphasise the complexity of the factors influencing BC in female football players. Personalising and periodising carbohydrate intake and monitoring training loads are crucial to prevent adverse effects like higher %BF and muscle catabolism. Establishing healthy nutritional practices is essential for long-term health and performance.