This study aimed to observe adolescents’ changes and individual responses regarding the anthropometry, cardiometabolic profile, vitamin D concentrations, physical fitness, and motor competence upon immediate return and three months of school activities after lockdown. Methods: The study included 28 adolescents (14.8 ± 0.8 years) of both sexes. Anthropometric measures, body composition, cardiometabolic parameters, physical fitness, and motor competence were assessed. A paired t-test was used to compare the frequencies of respondents and the effect size of the results, considering significant p < 0.05. Results: After three months of school activities, adolescents changed their body composition, reducing % fat mass (p = 0.008) and increasing fat-free mass (p = 0.008). In terms of physical fitness, there was increased abdominal resistance (p < 0.001; ES = −0.42) and motor performance, with reduction in supine-to-stand test time (p < 0.001; ES = 0.53). There were very beneficial effects in reducing resting heart rate (p ≤ 0.001; ES = 0.61) and increasing vitamin D concentrations (p < 0.001; ES = −0.61). After three months of a school routine, the proportions of change in respondents were similar between girls and boys and eutrophic individuals and overweight individuals. Conclusions: Returning to school activities after lockdown was important for the recovery of vitamin D concentrations, physical fitness, and motor competence, whose responses were independent of the level of adiposity and sex of the adolescents.
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