We conducted a prospective population-based cohort study to assess risk factors for infection, hospitalization, and death from SARS-CoV-2. The study comprised the people covered by the Health Service of Navarre, Spain. Sociodemographic variables and chronic conditions were obtained from electronic healthcare databases. Confirmed infections, hospitalizations, and deaths from SARS-CoV-2 were obtained from the enhanced epidemiological surveillance during the second SARS-CoV-2 epidemic surge (July-December 2020), in which diagnostic tests were widely available. Among 643,757 people, 5497 confirmed infections, 323 hospitalizations, 38 intensive care unit admissions, and 72 deaths from SARS-CoV-2 per 100,000 inhabitants were observed. A higher incidence of confirmed infection was associated with people aged 15-29 years, nursing home residents, healthcare workers, people born in Latin America or Africa, as well as in those diagnosed with diabetes, cardiovascular disease, chronic obstructive pulmonary disease (COPD), chronic kidney disease, dementia, severe obesity, hypertension and functional dependence. The risk of hospitalization in the population was associated with males, higher age, nursing home residents, Latin American or African origin, and those diagnosed with immunodeficiency, diabetes, cardiovascular disease, COPD, asthma, kidney disease, cerebrovascular disease, cirrhosis, dementia, severe obesity, hypertension and functional dependence. The risk of death was associated with males, higher age, nursing home residents, Latin American origin, low income level, immunodeficiency, diabetes, cardiovascular disease, COPD, kidney disease, dementia, and functional dependence. This study supports the prioritization of the older population, nursing home residents, and people with chronic conditions and functional dependence for SARS-CoV-2 prevention and vaccination, and highlights the need for additional preventive support for immigrants.