The widespread use of wearable devices has enabled continuous monitoring of biometric data, including heart rate variability (HRV) and resting heart rate (RHR). However, the validity of these measurements, particularly from consumer devices like Apple Watch, remains underexplored. This study aimed to validate HRV measurements obtained from Apple Watch Series 9 and Ultra 2 against the Polar H10 chest strap paired with the Kubios HRV software, which together served as the reference standard. A prospective cohort of 39 healthy adults provided 316 HRV measurements over a 14-day period. Generalized Estimating Equations were used to assess the difference in HRV between devices, accounting for repeated measures. Apple Watch tended to underestimate HRV by an average of 8.31 ms compared to the Polar H10 (p = 0.025), with a mean absolute percentage error (MAPE) of 28.88% and a mean absolute error (MAE) of 20.46 ms. The study found no significant impact of RHR discrepancies on HRV differences (p = 0.156), with RHR showing a mean difference of −0.08 bpm, an MAPE of 5.91%, and an MAE of 3.73 bpm. Equivalence testing indicated that the HRV measurements from Apple Watch did not fall within the pre-specified equivalence margin of ±10 ms. Despite accurate RHR measurements, these findings underscore the need for improved HRV algorithms in consumer wearables and caution in interpreting HRV data for clinical or performance monitoring.