Background: Although there is consistent evidence of unhealthy changes in the 24-hour movement behaviours when comparing pre-COVID-19 periods to the early stages of the pandemic, there is limited research on long-term changes among adolescents. This study aimed to analyze both between- and within-participant differences in accelerometer-assessed 24-hour movement behaviours by comparing cross-sectional and prospective data from the pre-COVID-19 period (August to December 2019) to the period following the reopening of schools for in-person classes in southern Brazil (August to December 2022). Methods: This is a repeated cross-sectional with a nested cohort study. The 24-hour movement behaviours (i.e., time spent in physical activity of light [LIPA] and moderate-to-vigorous [MVPA] intensities, sedentary behaviour [SB], and sleep time [SPT]) were assessed by processing raw accelerometer data derived from a 24-hour/7-day wrist-worn protocol. Compositional multilevel models were applied to compare the 24-hour movement behaviour composition between time points for both cross-sectional and prospective data. Self-reported sociodemographic characteristics were examined as potential moderators. Results: The cross-sectional and prospective samples comprised, respectively, 1276 (53% female, average age of 16.4 ± 1.1) and 249 (53% female, average age of 15.6 ± 0.8) participants. The 24-hour movement behaviour composition differed between time-points in the cross-sectional (p<0.001) and prospective samples (p<0.001). Differences from 2019 to 2022 were explained by lower MVPA (-3.3 and -5.4 min/day in cross-sectional and prospective analysis, respectively) and a higher SB (4.7 and 34 min/day in cross-sectional and prospective analysis, respectively). No significant differences were observed for LIPA and SPT. Conclusions: Differences in the 24-hour movement behaviour composition comparing the cross-sectional samples, although statistically significant, were considered trivial and unlikely to have a substantial practical impact. However, considerable differences were observed in the prospective analysis. Taken together, the results suggest that most of the observed changes over time were expected as a natural consequence of aging during high school, with only a small portion attributable to the residual impact of the pandemic.