Introduction: Football was the first sport to resume competitions after the coronavirus disease 2019 (COVID-19) lockdown and promptly the hypothesis was raised of a potential relationship between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and musculoskeletal injuries in athletes. This study aimed to confirm the association between SARS-CoV-2 infection and muscle strain injury in a large population of elite football players and to investigate if the COVID-19 severity level could affect the risk of injury. Methods: A retrospective cohort study involving 15 Italian professional male football teams was performed during the Italian Serie A 2020–2021 season. Injuries and SARS-CoV-2 positivity data were collected by team doctors through an online database. Results: Of the 433 included players, we observed 173 SARS-CoV-2 infections and 332 indirect muscle strains. COVID-19 episodes mostly belonged to severity level I and II. The injury risk significantly increased after a COVID-19 event, by 36% (HR = 1.36, CI95% 1.05; 1.77, p-value = 0.02). The injury burden demonstrated an 86% increase (ratio = 1.86, CI95% 1.21; 2.86, p-value = 0.005) in the COVID-19 severity level II/III versus players without a previous SARS-CoV-2 infection, while level I (asymptomatic) patients showed a similar average burden (ratio = 0.92, CI95% 0.54; 1.58, p-value = 0.77). A significantly higher proportion of muscle–tendon junction injuries (40.6% vs. 27.1%, difference = 13.5%, CI95% 0.002%; 26.9%, p-value = 0.047) was found when comparing level II/III versus Non-COVID-19. Conclusions: This study confirms the correlation between SARS-CoV-2 infection and indirect muscle injuries and highlights how the severity of the infection would represent an additional risk factor.