Injuries are one of the most significant issues for elite football players. Consequently, elite football clubs have been consistently interested in having practical, interpretable, and usable models as decision-making support for technical staff. This study aimed to analyze predictive modeling of injury risk based on body composition variables and selected physical fitness tests for elite football players through a sports season. The sample comprised 36 male elite football players who competed in the First Portuguese Soccer League in the 2020/2021 season. The models were calculated based on 22 independent variables that included players’ information, body composition, physical fitness, and one dependent variable, the number of injuries per season. In the net elastic analysis, the variables that best predicted injury risk were sectorial positions (defensive and forward), body height, sit-and-reach performance, 1 min number of push-ups, handgrip strength, and 35 m linear speed. This study considered multiple-input single-output regression-type models. The analysis showed that the most accurate model presented in this work generates an error of RMSE = 0.591. Our approach opens a novel perspective for injury prevention and training monitorization. Nevertheless, more studies are needed to identify risk factors associated with injury prediction in elite soccer players, as this is a rising topic that requires several analyses performed in different contexts.