Resting heart rate (HR) and HR variability (HRV) are widely used parameters to assess cardiac autonomic nervous system function noninvasively. While resting assessments can be performed during sleep or after awakening, it would be relevant to know how interchangeable the results of these measurements are. This study aimed at examining the alignment between nocturnal and morning assessments during regular endurance training and in response to intensive training. A total of 24 recreational runners performed a 3-week baseline period (BL) and a 2-week overload (OL) period (Lucia's training impulse + 80%). Their running performance was assessed with a 3000-m running test after the BL and OL. The participants recorded daily their nocturnal HR and HRV (the natural logarithm of the root mean square of successive differences; LnRMSSD) with a photoplethysmography-based wrist device and performed an orthostatic test (2-min supine, 2-min standing) every morning with a chest-strap HR sensor. The HR and LnRMSSD segments that were analyzed from the nocturnal recordings included start value (SleepStart), end value (SleepEnd), first 4-h segment 30min after detected sleep onset (Sleep4h), and full sleep time (SleepFull). The morning segments consisted of the last-minute average in both body positions. All segments were compared at BL and in response to the 3000-m test and OL. All nocturnal HR and LnRMSSD segments correlated with supine and standing segments at BL (r = 0.42 to 0.91, p < 0.05). After the 3000-m test, the HR increased and LnRMSSD decreased only in the SleepStart, Sleep4h, and SleepFull segments (p < 0.05). In response to the OL, the standing HR decreased (p < 0.01), while the LnRMSSD increased (p < 0.05) in all segments except for SleepStart. The Pearson correlations between relative changes in nocturnal and morning segments were - 0.11 to 0.72 (3000-m) and - 0.25 to 0.79 (OL). The OL response in Sleep4h HR and LnRMSSD correlated with the relative change in 3000-m time (r = 0.63, p = 0.001 and r=-0.50, p = 0.013, respectively). Nocturnal and morning HR and LnRMSSD correlated moderately or highly in the majority of cases during the BL, but their responses to intensive training were not similarly aligned, especially in LnRMSSD. The nocturnal segments seemed to be sensitive to physical loading, and their responses were associated with the performance-related training responses.