Although SARS-CoV-2 vaccination reduces hospitalization and mortality, its long-term impact on Long-COVID remains to be elucidated. The aim of the study was to evaluate the different development of Long-COVID clinical phenotypes according to the vaccination status of patients. Clinical and demographic characteristics were assessed for each patient, while Long-COVID symptoms were self-reported and later stratified into distinct clinical phenotypes. Vaccination was significantly associated with the avoidance of hospitalization, less invasive respiratory support, and less alterations of cardiopulmonary functions, as well as reduced lasting lung parenchymal damage. However, no association between vaccination status and the development of at least one Long-COVID symptom was found. Nevertheless, clinical phenotypes were differently associated with vaccination status, as neuropsychiatric were more frequent in unvaccinated patients and cardiorespiratory symptoms were reported mostly in vaccinated patients. Different progression of disease could be at play in the different development of specific Long-COVID clinical phenotypes, as shown by the different serological responses between unvaccinated and vaccinated patients. A higher anti-Spike (