This study examined the impact of dynamic workstations, specifically sit-stand desks and under-the-desk bikes, on physiological stress using Heart Rate Variability (HRV) measurements. The research aimed to understand how these workstations influence occupational stress, particularly considering sex differences. Seven full-time employees participated in three conditions: original workstation (PRE), dynamic workstation without the use of its gamified app (DBN), and dynamic workstation with its gamified app (DBG). ECG data was collected for HRV analysis during each condition and HRV parameters analyzed included SDNN, RMSSD, and SI. Results indicated significant differences in HRV parameters between conditions, with lower RMSSD observed in the dynamic workstation condition DBN compared to PRE. Sex differences were noted in SDNN and SI parameters with females showing lower HRV, indicating higher physiological stress, emphasizing the importance of considering sex when assessing the impact of dynamic workstations on physiological stress. These findings support the potential for dynamic workstations to be integrated into office environments to manage stress and improve employee well-being.