There are theoretical and experimental bases to assume that hormone fluctuations throughout the menstrual cycle (MC) can influence recovery, but a consensus has not yet been reached. The purpose of the present study was to investigate how the MC phases influence resting heart rate (HR), subjective sleep quality, physical and mental readiness to train among endurance athletes. Secondly, the study described the potential differences in recovery between ovulatory and anovulatory cycles. Fifteen naturally menstruating endurance athletes recorded daily recovery measures for 2 ± 1 MCs. Resting HR was assessed using night-recording watches or a standardized procedure upon awakening; subjective self-report measures of sleep quality, physical and mental readiness to train were assessed with a visual analogue scale (1-10). Four MC phases with a duration of three days each were determined using the calendar-based counting method and the urinary ovulation prediction test: early follicular phase (EFP) (day 1 to day 3 of MC), late follicular and ovulatory phase (OP) (three days ending with and first three days following a positive ovulation test), mid-luteal phase (MLP) (7 - 9 days following a positive ovulation test). Data were analyzed using mixed-effects modelling. Resting HR was significantly higher in ovulatory compared to anovulatory cycles (p = .020), without a significant change between MC phases. MC phase had a significant influence on the subjective recovery measures: subjective sleep quality was decreased in the OP (p = .006) and MLP (p = .006), physical and mental readiness to train were worse in MLP (p = .030; p < 0.001) compared to EFP. Increased MC-related perceived side effects were associated with reduced mental readiness to train (p = .024). These findings indicate that the MC should be accounted for when monitoring recovery, as MC phase, including MC-related side effects and menstrual disturbances, can influence recovery.