Objectives: Exercise-induced muscle damage (EIMD) can impair muscle function and subsequent athletic performance. This study examined whether an isonitrogenous yeast protein–whey protein composite (YP) modifies recovery from EIMD compared with whey protein (WP) and a water-only control (C) in well-trained athletes. Methods: In this prospective, randomized, three-arm trial, 54 athletes were allocated to YP, WP, or C; 48 completed all follow-up procedures. YP and WP provided 0.9 g·kg−1·day−1 of actual protein, whereas C received water only and was not energy or sensory matched to the protein interventions. After 7 days of supplementation, participants completed a bilateral isokinetic EIMD protocol; supplementation continued through the 48 h assessment. Outcomes were assessed before EIMD, immediately afterward, and at 24, 48, and 72 h and were organized into muscle damage and soreness, inflammatory responses, and muscle function and performance. Female and male athletes were analyzed separately using linear mixed-effects models with multiplicity-adjusted contrasts. The study was not powered to formally compare intervention effects between sexes. Results: EIMD produced time-dependent biochemical, perceptual, and functional changes. Holm-adjusted comparisons showed lower CK in YP than C at 24 h in females and 48 h in males. The female 24 h CK finding was considered exploratory because the corresponding group × time interaction did not remain significant after damage-domain BH-FDR correction; the immediate male YP–C difference was significant only in the log-scale analysis. In males, YP was associated with lower soreness averaged across assessments and a lower immediate post-EIMD IL-6 value than C. Selected male CMJ comparisons favored YP but were exploratory after broader multiplicity correction. Acute-decline analyses showed smaller losses with YP in bilateral MVC and right-leg eccentric peak torque in males; only the right-leg eccentric YP–C comparison remained significant after BH-FDR correction. Conclusions: Compared with water alone, YP favorably influenced selected biochemical, perceptual, and muscle-function responses following EIMD, with the clearest pattern observed in the male analysis. Its overall response pattern was broadly aligned with WP, supporting the recovery-related potential and practical value of incorporating yeast-derived protein into a whey-based formulation.
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