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The objective of this study was to analyze the psychological responses of the Brazilian population and understand their level of anxiety, depression, and stress during different times of the COVID-19 pandemic, as well as how the PA level and sociodemographic aspects may have influenced them. This longitudinal study collected data in two periods: April/May 2020 (T1) at the beginning of the COVID-19 pandemic with restrictions and social distancing indication (during the lockdown), and October/November 2021 (T2) period with fewer restrictions and vaccines available in Brazil (after the lockdown). Data were collected online, including sociodemographic information (age, gender, education), mental health by the Depression, Anxiety, and Stress Scale (DASS-21), and estimated PA levels using the International Physical Activity Questionnaire (IPAQ) short version. Statistical analysis used generalized linear regression models to evaluate the impact of time, sociodemographic aspects, and PA on the risk of depression, anxiety, and stress between periods. Adjusted risk probabilities and Odds Ratio (OR) with 95% confidence intervals (95% CI) were calculated with a 5% significance level. Comparisons between T2 and T1 showed an increased risk for depression (OR=1.48 [95%CI=1.03;2.12]), anxiety (2.66 [1.70;4.17]), and stress (1.95 [1.36;2.79]). Low PA levels were associated with a higher risk of depression (2.08 [1.14;3.82]) and stress (2.03 [1.09;3.80]) but not anxiety in the comparison between T2 and T1. The findings highlight the increased risk for depression, anxiety, and stress in T2 and suggest PA promotion as a possibility for mental health care.