Purpose: We aimed to determine the effects of 12 weeks of soy milk consumption combined with resistance training (RT) on body composition, physical performance, and skeletal muscle regulatory markers in older men. Methods: In this randomized clinical trial study, 60 healthy elderly men (age = 65.63 ± 3.16 years) were randomly assigned to four groups: resistance training (RT; n =  15), soy milk consumption (SMC; n  =  15), resistance training + soy milk (RSM; n = 15), and control (CON; n  =  15) groups. The study was double-blind for the soy milk/placebo. Participants in RT and RSM groups performed resistance training (3 times/week) for 12 weeks. Participants in the SMC and RSM groups consumed 240 mL of soy milk daily. Body composition [body mass (BM), body fat percent (BFP), waist-hip ratio (WHR), and fat mass (FM)], physical performance [upper body strength (UBS), lower body strength (LBS), VO2max, upper anaerobic power, lower anaerobic power, and handgrip strength], and serum markers [follistatin, myostatin, myostatin-follistatin ratio (MFR), and growth and differentiation factor 11 (GDF11)] were evaluated before and after interventions. Results: All 3 interventions significantly (p < 0.05) increased serum follistatin concentrations (RT = 1.7%, SMC = 2.9%, RSM = 7.8%) and decreased serum myostatin (RT = −1.3% SMC = −5.4%, RSM = −0.5%) and GDF11 concentrations (RT = −1.4%, SMC = −1.4%, RSM = -9.0%), and MFR (RT = −2.6%, SMC = −3.2%, RSM = −12%). In addition, we observed significant reduction in all 3 intervention groups in BFP (RT = −3.6%, SMC = −1.4%, RSM = −6.0%), WHR (RT = −2.2%, SMC = −2.1%, RSM = −4.3%), and FM (RT = −9.6%, SMC = −3.8%, RSM = −11.0%). Moreover, results found significant increase only in RT and RSM groups for muscle mass (RT = 3.8% and RSM = 11.8%), UBS (RT = 10.9% and RSM = 21.8%), LBS (RT = 4.3% and RSM = 7.8%), upper anaerobic power (RT = 7.8% and RSM = 10.3%), and lower anaerobic power (RT = 4.6% and RSM = 8.9%). Handgrip strength were significantly increased in all 3 intervention groups (RT = 7.0%, SMC = 6.9%, RSM = 43.0%). VO2max significantly increased only in RSM (1.7%) after 12 weeks of intervention. Additionally, significant differences were observed between the changes for all variables in the RSM group compared to RT, SMC, and CON groups (p < 0.05). Conclusions: There were synergistic effects of soy milk and RT for skeletal muscle regulatory markers, body composition, and physical performance. Results of the present study support the importance of soy milk in conjunction with RT for older men.