Introduction: Low Energy Availability (Low EA, LEA, <30 kcal·kg⁻¹ fat free mass·day⁻¹) is the underlying mechanism of Relative Energy Deficiency in Sport (REDs), yet its acute autonomic correlates at the day-to-day level remain insufficiently characterized. We quantified the within-person association between daily EA and next-night nocturnal Heart Rate Variability (HRV) in 22 physically active individuals (BUT CGM dataset) who experienced both LEA and adequate EA (≥45 kcal·kg⁻¹ fat free mass·day⁻¹) days during 8–10 days of free-living monitoring (123 person-day observations; 71 LEA, 52 adequate EA). Methods: Daily EA was computed as (energy intake-exercise energy expenditure)/fat-free mass. Exercise energy expenditure was estimated from a cardiopulmonary exercise testing (CPET) calibrated zone-based model using individual ventilatory thresholds. Nocturnal HRV was extracted from single-lead ECG during sleep, computed on 5-minute segments and averaged across the night; each night was paired with the preceding day's EA. Results: Using linear mixed-effects models with random intercepts for participants, eight of nine HRV parameters were significantly elevated on adequate EA versus LEA days: pNN50, HF power, RMSSD, standard deviation of heart rate (SDHR), SDNN, LF power, lnRMSSD, and RR intervals. The LF/HF ratio did not differ. Conclusion: A single day of LEA was followed by reduced nocturnal cardiac autonomic activity compared with the same individual's Adequate EA days. These findings suggest that adequate daily energy availability may be important for next-night parasympathetic recovery. Although nocturnal HRV cannot replace direct assessment of EA, repeated overnight measurements may provide a useful non-invasive signal of recent energy status.