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Platelet-rich plasma (PRP) injections are extremely popular in the management of sports injuries in elite athletes. However, data on the use of various administration protocols of PRP are contradictory. The efficacy of platelet-rich plasma in the treatment of muscle injuries in professional soccer players has to be contextualized within the sport-specific rehabilitation program. Despite the questionable role of PRP, a well-structured rehabilitation program is still regarded as the gold standard. We examined the efficacy of various PRP protocols in the management of muscle injuries in professional soccer players in respect to treatment duration and injury recurrence. A retrospective cohort study. Muscle injuries in professional soccer players (n = 79, height 182.1 ± 5.9 cm, weight 76.8 ± 5.8 kg, BMI 23.1 ± 1.4 kg/m2) from three elite soccer clubs from the Russian Premier League were recorded during the 2018–2019 season. The injuries were graded based on MRI, using the British Athletic Muscle Injury Classification. Treatment protocols included the POLICE regimen, short courses of NSAID administration, and the specific rehabilitation program. The sample group of players were administered PRP injections. The average treatment duration with PRP injection was significantly longer than conventional treatment without PRP, 21.5 ± 15.7 days and 15.3 ± 11.1 days, respectively (p = 0.003). Soccer-specific rehabilitation and obtaining MRI/US before the treatment was associated with significantly reduced injury recurrence rate (p < 0.001). There was no significant difference between the PRP injection protocol applied to any muscle and the treatment duration in respect of grade 2A–2B muscle injuries. The total duration of treatment of type 2A–2B injuries was 15 days among all players. In the group receiving local injections of PRP, the total duration of treatment was 18 days; in the group without PRP injections, the treatment duration was 14 days. In our study, PRP treatment was associated with longer treatment duration, regardless of which muscle was injured. This may reflect the tendency to use PRP in higher-degree injuries. Soccer-specific rehabilitation significantly reduced the injury recurrence rate when compared to the administration of PRP injections. MRI/US imaging before returning to play was also associated with a lower injury recurrence rate. There was no significant difference between the PRP injection protocol applied to any muscle and the treatment duration in treatment of type 2A–2B muscle injuries.