Effective vaccination against coronavirus (COVID) mitigates the risk of hospitalizations and mortality but it is unclear whether the vaccination status may influence the post-COVID symptoms in patients who required hospitalization. The available evidence is limited to outpatients with mild cases. Here, we evaluated 412 patients (age: 60 ± 16 years, 65% males) consecutively admitted at two Hospitals in Brazil due to a confirmed case of COVID-19. As compared to patients with complete vaccination (n = 185) before infection/hospitalization, those with no/incomplete vaccination (n = 227) were younger and had a lower frequency of several comorbidities. Data during hospitalization revealed that the no/incomplete vaccination group required more admissions in the intensive care unit, used more corticosteroids and had higher rates of pulmonary embolism/deep venous thrombosis than the complete vaccination group. At 90 days after hospital discharge, patients with no/incomplete vaccination presented a higher frequency of ≥ 1 symptom than patients with complete vaccination: 40 vs. 27%; p = 0.013. After adjustments for confounders, no/incomplete vaccination (OR = 1.819; 95% CI:1.175–2.815), females (OR = 2.435; 95% CI:1.575–3.764) and intensive care unit admission during hospitalization (OR = 1.697; 95% CI:1.062–2.712) were independently associated with ≥ 1 symptom 90-days after hospital discharge. In conclusion, even in patients with more severe COVID-19 infection, vaccination mitigate the probability of long-COVID symptoms.