Abstract: Sleeping problems can affect physiological adaptations and the recovery process. The aim of this study was to analyse the effect of the intensity and the hour of the training session on sleep quality and cardiac autonomic activity in amateur ultra-endurance athletes. We used a comparative, randomized crossover design to test the effect of moderate (M) or vigorous (V) intensity and morning (m) or evening (e) training journey, separated by 72 h of recovery, on actigraphic and subjective sleep quality and nocturnal cardiac autonomic activity in fourteen ultra-endurance male runners. No significant differences among training sessions were found in nocturnal heart rate variability or in subjective sleep quality, but participants experienced significantly higher calm sleep after Mm than Me (p = 0.028; ES = 0.7) and more refreshed after awakening when they performed a Me than Vm (p = 0.04; ES = 0.6). Higher sleep efficiency was found when the training is performed in the morning compared to the evening sessions in both intensities, and it was also observed in Me vs Ve (p = 0.012; ES = 0.8). Significantly lower numbers of awakenings were observed when the training was performed in the morning, and actual sleep time was significantly lower when participants performed a vigorous training session compared to a moderate one (Vm vs Mm: p = 0.035; ES = 0.6; Ve vs Mm: p = 0.036; ES = 0.6). Moderate exercise performed in the morning had a higher sleep efficiency compared to other types of training and intensity training is more important than the time of the day of training on sleep quality.