The global health emergency caused by COVID-19 concluded in May 2023, marking the beginning of an endemic phase. This study aimed to evaluate the association between vaccination status and other patient characteristics and the risk of severe disease during this new endemic period. A nationwide cohort study was conducted in Mexico, where we analyzed data from 646 adults who had received positive confirmation of COVID-19 through PCR testing from May to August 2023. The overall risk of severe symptoms in the study sample was 5.3%. The average time elapsed from the last vaccine shot to symptom onset was over six months in all the immunized groups (1, 2 or 3 vaccine doses). Compared to unvaccinated patients, those with three vaccine doses showed an elevated risk of severe symptoms. Advancing age and various chronic comorbidities (specifically cardiovascular, kidney, and obstructive pulmonary conditions) were associated with a heightened risk of severe COVID-19 manifestations. These findings underscore the ongoing seriousness of COVID-19, even in an endemic phase, underscoring the urgent need for tailored interventions aimed at high-risk patients.