Sympathetic (fight-or-flight) activation is necessary for vigorous physical activity, therefore it's natural for your HRV to be low when you're exercising. Think of it this way: As your heart rate accelerates to pump more oxygenated blood throughout your body to power your muscles, your heart beats more like a fast metronome. Therefore, the variation in milliseconds between consecutive heartbeats (a.k.a., your heart rate variability) will go down as your heart rate climbs.

Exercising is essentially putting an intentional amount of stress on your body, which will be reflected in lower HRV during the activity, as well as potentially afterwards. To maintain fitness and health over the long run, we benefit from periods of physical stress and recovery. Failing to adequately push your body through exercise hinders adaptation, growth, and improvement. Thus, occasionally stressing out your body through workouts can ultimately help promote long-term growth and adaptation. Over the long term, consistent exercise contributes to higher HRV.