BACKGROUND: The resistance training with blood flow restriction (BFR) presents results in strength gain and muscle hypertrophy. However, there are no data that evaluate the long-term adaptation of the autonomic nervous system and its influence on the performance, especially with eccentric contractions. OBJECTIVE: To perform a systematic autonomous monitoring during eccentric training with BFR at different loads and to correlate them with possible changes in the performance METHODS: This is a 4-arms, randomized controlled and single blind trial. Sixty men were randomized in four groups: low and high load eccentric exercise (LL and HL); LL and HL with BFR (LL-BFR and HL-BFR). The participants underwent 18 sessions of eccentric exercise for the dominant quadriceps femoris muscle in the isokinetic dynamometer. The performance (strength through isometric, concentric and eccentric peaks torque on the isokinetic dynamometer and Single-leg Hop Test) was evaluated 1 week before, in the fourth week and 1 week after the end of the training programme. Heart rate variability (HRV) through vagal and global indices was evaluated daily for 15 min before each session. RESULTS: There was a significant correlation between performance and HRV for LL and HL-BFR groups, with an increase in parasympathetic indices in the first group and an increase in performance in the second group. CONCLUSION: HRV indices are correlated with performance. However, in the LL group, there was an increase in parasympathetic indices without repercussions on performance while, in the HL-BFR group, there was an increase in performance and no repercussion in the autonomic indices.