The omicron (B.1.1.529) variant of SARS-CoV-2 has increased capacity to elude immunity and cause breakthrough infections. The aim of this study was to estimate the effectiveness of mRNA-based vaccine boosters (third dose) against infection with the omicron variant by age, sex, time since complete vaccination, type of primary vaccine, and type of booster. In this nationwide cohort study, we linked data from three nationwide population registries in Spain (Vaccination Registry, Laboratory Results Registry, and National Health System registry) to select community-dwelling individuals aged 40 years or older, who completed their primary vaccine schedule at least 3 months before the start of follow-up, and had not tested positive for SARS-CoV-2 since the start of the pandemic. On each day between Jan 3, and Feb 6, 2022, we matched individuals who received a booster mRNA vaccine and controls of the same sex, age group, postal code, type of vaccine, time since primary vaccination, and number of previous tests. We estimated risk of laboratory-confirmed SARS-CoV-2 infection using the Kaplan-Meier method and compared groups using risk ratios (RR) and risk differences. Vaccine effectiveness was calculated as one minus RR. Between Jan 3, and Feb 6, 2022, 3 111 159 matched pairs were included in our study. Overall, the estimated effectiveness from day 7 to 34 after a booster was 51·3% (95% CI 50·2–52·4). Estimated effectiveness was 52·5% (51·3–53·7) for an mRNA-1273 booster and 46·2% (43·5–48·7) for a BNT162b2 booster. Effectiveness was 58·6% (55·5–61·6) if primary vaccination had been with ChAdOx1 nCoV-19 (Oxford–AstraZeneca), 55·3% (52·3–58·2) with mRNA-1273 (Moderna), 49·7% (48·3–51·1) with BNT162b2 (Pfizer–BioNTech), and 48·0% (42·5–53·7) with Ad26.COV2.S (Janssen). Estimated effectiveness was 43·6% (40·0–47·1) when the booster was administered between 151 days and 180 days after complete vaccination and 52·2% (51·0–53·3) if administered more than 180 days after primary scheduled completion. Booster mRNA vaccine-doses were moderately effective in preventing infection with the omicron variant of SARS-CoV-2 for over a month after administration, which indicates their suitability as a strategy to limit the health effects of COVID-19 in periods of omicron variant domination. Estimated effectiveness was higher for mRNA-1273 compared with BNT162b2 and increased with time between completed primary vaccination and booster. None.