This study investigated the relationship between well-being indices and the session rating of perceived exertion (session-RPE), recovery (TQR), and physical enjoyment (PE) during intensified, tapering phases of judo training. Sixty-one judo athletes (37 males, ranges 14–17 years, 159–172 cm, 51–67 kg) were randomly assigned to three experimental (i.e., randori, uchi-komi, running) and control groups (regular training). Experimental groups trained four times per week for 4 weeks of intensified training followed by 12 days of tapering. Session-RPE, well-being indices (i.e., sleep, stress, fatigue, delayed onset of muscle soreness (DOMS), Hooper index (HI)), and TQR were measured every session, whereas PE was recorded after intensified, tapering periods. Recovery (TQR) was negatively correlated with sleep, stress, fatigue, DOMS, HI, session-RPE in intensified period and was negatively correlated with sleep, stress, fatigue, DOMS, HI in tapering. Session-RPE was positively correlated with sleep, fatigue, DOMS, HI in intensified period and positively correlated with fatigue, DOMS in tapering. PE was negatively correlated with stress in intensified training. Enjoyment could be partially predicted by sleep only in intensified periods. Session-RPE could be partially predicted by TQR, fatigue during intensified periods and by sleep, and HI during tapering. Sleep, recovery state, pre-fatigue states, and HI are signals contributing to the enjoyment and internal intensity variability during training. Coaches can use these simple tools to monitor judo training.