People living with HIV (PLWH) are prioritised for SARS-CoV-2 vaccination due to their vulnerability to severe COVID-19. Therefore, the epidemiological surveillance of vaccination coverage and the timely identification of suboptimally vaccinated PLWH is vital. We assessed SARS-CoV-2 vaccination coverage and factors associated with under-vaccination among PLWH in Catalonia, Spain. As of 11.12.2021, 9945/14942 PLWH (66.6%) had received ≥1 dose of a SARS-CoV-2 vaccine. Non-Spanish origin (adjusted odds ratio (aOR) 0.64, 95% CI 0.59−0.70), CD4 count of 200−349 cells/μL (aOR 0.74, 95% CI 0.64−0.86) or 350−499 cells/μL (aOR 0.79, 95% CI 0.70−0.88), detectable plasma HIV-RNA (aOR 0.61 95% CI 0.53−0.70), and previous SARS-CoV-2 diagnosis (aOR 0.58 95% CI 0.51−0.65) were associated with under-vaccination. SARS-CoV-2 diagnosis (437 9.5% vs. 323 3.5%, p < 0.001), associated hospitalisations (10 2.3% vs. 0 0%, p < 0.001), intensive care unit admissions (6 1.4% vs. 0 0%, p < 0.001), and deaths (10 2.3% vs. 0 0%, p < 0.001) were higher among unvaccinated PLWH. Vaccination coverage was lower among PLWH with a CD4 count >200 cells/μL, detectable plasma HIV-RNA, previous SARS-CoV-2 diagnosis, and migrants. SARS-CoV-2 diagnosis, associated hospitalisations, and deaths among PLWH were lower among the vaccinated compared with the unvaccinated. SARS-CoV-2 vaccination prioritisation has not completely reached vulnerable PLWH with poorer prognosis. This information can be used to inform public health strategies.