(1) Background: Soccer accounts for 30% of all sports injuries. Muscle injuries in soccer, not caused by trauma or contact, are the most common. The objective was to assess the risk of injury based on the footwear used by soccer players and the playing field and to identify the best predictive model of muscle injuries; (2) Methods: An ambispective cohort study. The primary variable was the number of muscle injuries in the last three seasons. The secondary variables were age, body mass index, type of soccer shoes and turf, training load and position on the field. The possible confounding variables were motivation for the choice of footwear, date of injuries, time playing and regular first-team player status; (3) Results: 156 players were recruited. The risk of injury is 1.03 (95% CI: 0.83; 1.27) times more frequent in players competing on artificial turf. The risk of injury is slightly higher in first-team players than in substitutes (RR = 1.02; 95% CI: 0.79; 1.32). There was no statistically significant relationship between the position on the field (p = 0.91), the type of shoe (p = 0.69) and the motivation to buy the shoes (p = 0.82), regarding the risk of muscle injury in these athletes. The best model to estimate risk of injury includes age, training load and soccer shoe type as confounding variables (AIC = 190.5; p = 0.10; χ2(3) = 10.14; p = 0.02); (4) Conclusions: The risk of muscle injury is higher in non-professional soccer players competing on artificial pitches and in those who are regular starters on their teams. Field position, soccer shoe and motivation to purchase the soccer shoe are variables that do not increase the risk of muscle injury in these athletes. The best predictive model of injury includes age, training load and shoe type.