The aim of this study was to evaluate the mediation role of muscle quantity in the relationship between physical fitness and cardiometabolic risk factors (CMRF) in adolescents. This cross-sectional study conducted with 120 adolescents of both sexes, aged between 10 and 17 years. Body mass, height, fat mass (FM), lean mass, blood pressure, high-density lipoprotein, low-density lipoprotein, triglycerides, glucose, insulin, cardiorespiratory fitness (CRF) and 1 repetition maximum strength (1-RM) with evaluation of the leg press 45° (RM-leg), bench press (RM-bench) and arm curl (RM-arm). Body mass index z-score, appendicular skeletal muscle mass, appendicular skeletal muscle mass index, lean mass index (LMI), muscle-to-fat ratio (MFR), age at peak height velocity, and CMRF z-score were calculated. The direct relation between FM and CMRF was mediated by the LMI (26%) and inverse relation between CRF and CMRF was mediated by the LMI (26%). For girls, the direct relation between FM and CMRF was mediated by the LMI (32%); the inverse relation between CRF, RM-leg, RM-arm and CMRF was mediated by the LMI (32%, 33%, and 32%, respective). For boys, the indirect effect was not significant, indicating that LMI is not a mediator in the relation between FM, CRF, 1-RM with CMRF. The direct relation between RM-leg and CMRF was mediated by the MRF (16%). This finding evidenced the importance of promoting a healthy lifestyle to improve physical fitness levels and the quantity of muscle mass in adolescents.