Regular exercise helps to mitigate psychological issues during stressful conditions, such as the COVID-19 lockdown. Since the mental health impact depends on the duration of social isolation, we aimed to characterize exercise routines and mental health after the first and second Portuguese COVID-19 lockdowns. A total of 27 Portuguese amateur athletes (AA, n = 11) and fitness enthusiasts (FE, n = 16) participated in a semi-structured interview. The results showed that both FE and AA experienced negative symptoms (stress, anxiety, depression, frustration, fatigue and saudade) during the first lockdown, which were reported as both barriers to and motivators for physical activity. Both groups managed to adapt to changes in daily schedules, the closure of sports facilities and a lack of social support by modifying their exercise routines. Strategies such as using music and social media networks were employed to enhance motivation and self-perception. We can conclude that mental health issues served both as barriers to and motivators for physical activity, and exercise was a valuable tool for overcoming the psychological consequences of the two lockdowns.