Purpose The three-minute all-out test (3MT), when performed on a laboratory ergometer in a linear mode, can be used to estimate the The aim of this study was to determine if machine learning models could predict the perceived morning recovery status (AM PRS) and daily change in heart rate variability (HRV change) of endurance athletes based on training, dietary intake, sleep, HRV, and subjective wellbeing measures. Methods Self-selected nutrition intake, exercise training, sleep habits, HRV, and subjective wellbeing of 43 endurance athletes ranging from Professional to recreationally trained were monitored daily for 12 weeks (3,572 days of tracking). Global and individualized models were constructed using machine learning techniques, with the single best algorithm chosen for each model. Model performance was compared with a baseline intercept-only model. Results Prediction error (root mean square error [RMSE]) was lower than baseline for the group models (11.8 vs. 14.1 and 0.22 vs. 0.29 for AM PRS and HRV change, respectively). At the individual level prediction accuracy outperformed the baseline model but varied greatly across participants (RMSE range 5.5 to 23.6 and 0.05 to 0.44 for AM PRS and HRV change, respectively). Conclusion At the group level daily recovery measures can be predicted based on commonly measured variables, with a small subset of variables providing most of the predictive power. However, at the individual level the key variables may vary, and additional data may be needed to improve prediction accuracy.