Background: The COVID-19 pandemic remains ongoing, with a significant number of survivors who have experienced moderate to severe clinical conditions and who have suffered great magnitude losses, especially in functional capacity, trigerring limitation on the daily autonomy and quality of life. Among the possibilities of intervention for the rehabilitation of the disease, physical/exercising training stands out, which can benefit several health outcomes and favours the adoption of healthier behaviors. Therefore, the aim of the study will be to analyze the effects of physical training on the functional, clinical, morphological, behavioral, and psychosocial status in adults and the elderly following COVID-19 infection. Methods: Randomized, controlled clinical trial, conducted in parallel, with the experimental group undergoing an intervention involving a multicomponent physical rehabilitation program, carried out at the Sports Center in partnership with the Academic Hospital of the Federal University of Santa Catarina, in Florianópolis, Brazil. Participants will be adults and elderly, of both sexes, in a post-COVID-19 infection state, who were hospitalized during the infection. The intervention will have a total duration of 24 weeks and will include a multicomponent physical training program, which will have gradual progression in frequency, duration, and intensity over the time. Regarding the outcomes, before, at the 12th and after 24 weeks of intervention, functional (primary outcome = functional index of aerobic capacity), clinical, morphological, behavioral, and psychosocial outcomes will be assessed. Discussion: This study will contribute to a greater understanding of the safety, adherence and benefits of physical training in the rehabilitation of post-COVID-19 patients. The results of this study will be disseminated through presentations at congresses, workshops, peer-reviewed publications, local and international conferences, especially with a view to proposing a post-COVID-19 Rehabilitation Care Protocol. Trial registration: This study was approved by the Ethics Committee in Research with Human Beings of the institution of origin (protocol 4.909.599) and registered in the Brazilian Registry of Clinical Trials (RBR-10y6jhrs), registered 22 February 2022, https://ensaiosclinicos.gov.br/rg/RBR-10y6jhrs.