Abstract Objective Studies in basic military training (BMT) examining sleep are largely cross-sectional, and do not investigate relationships between sleep, stress, recovery and fatigue. The aims of this study were to (1a) quantify changes in recruits’ sleep quantity and quality over 12 weeks of BMT; (1b) quantify changes in recruits’ perceptions of stress, fatigue and recovery over BMT; and (2) explore relationships between sleep, and perceptions of stress, fatigue and recovery. Methods 45 recruits (37 male; 8 female, age: 25.2 ± 7.2 years, height: 176.2 ± 10.0 cm, mass: 76.8 ± 15.0 kg) wore ActiGraph GT9X’s for 12 weeks of BMT, collecting sleep duration, efficiency and awakenings. Subjective sleep quality, fatigue were measured daily, with stress and recovery measured weekly. Multi-level models assessed relationships between sleep, and stress, recovery, and fatigue. Results Objective daily means for sleep duration were 6.3 h (± 1.2 h) and 85.6% (± 5.5%) for sleep efficiency. Main effects were detected for all mean weekly values (p < 0.05). Sleep quality showed the strongest relationships with stress, recovery and fatigue. The best model to explain relationships between, stress, recovery and fatigue, included sleep quality, sleep duration, sleep efficiency and awakenings. Conclusions The reported mean sleep duration of 6.3 h per night may negatively impact training outcomes across BMT. Combining both subjective and objective measures of sleep best explained relationships between sleep metrics stress, fatigue and recovery. Perceived sleep quality was most strongly related to change in stress, recovery, or post-sleep fatigue.