The purpose of this study was to compare hormonal, neuromuscular, and aerobic performance changes between a constant 2-minute interset recovery time and an interset recovery time based on individual heart rate (HR) responses during a 7-week (3 sessions per week, 3 × 10 repetition maximum [RM]) hypertrophic strength training period. The HR-dependent recovery time was determined with a Polar FT80 HR monitor, whereas the control groups used constant 2-minute periods between sets. From 24 male subjects who were divided in 2 equal groups, 21 completed the study (FT80, n = 12; CONTROL, n = 9). Serum blood samples analyzed for testosterone (TES) and cortisol (COR) were taken before and after the 7-week training period at rest. Concentric knee extension 1RM was measured before, after 4 weeks, and at the end of the training period. Concentric knee extension and knee flexion 10RM, central activation ratio (CAR), and maxVO2 were measured before and after the training. Serum TES concentrations were significantly higher after the training period in FT80 (p < 0.001), whereas no significant changes were observed in the CONTROL. Serum COR and maxVO2 were unchanged in both groups. In FT80 (p < 0.001), the increase in 10RM was higher (p < 0.05) than in CONTROL (p < 0.001). Central activation ratio increased in both groups, with the significant increase observed in FT80 (p < 0.05). The higher TES responses, 10RM, and CAR development in FT80 suggest that an HR-based recovery period system of the FT80 may be more efficient in this type of hypertrophic strength training (3 × 10RM). The protocol in this study may be considered as a metabolic training cycle that coaches and trainers can use within a longer periodized training program.