Lower COVID-19 vaccination coverage was observed among some populations with a migration background in the Netherlands. This study examined determinants of being unvaccinated against COVID-19 in the primary vaccination round in adults and in the 2022 autumn booster round in persons aged ≥60 years, among four populations of non-Dutch origin with below average vaccination coverage: Moroccan, Turkish, Surinamese and Dutch-Caribbean, and persons of Dutch origin. We performed a population-wide register-based study, examining associations between potential determinants and being unvaccinated using multivariable logistic regression and computing population attributable fractions. Being a migrant with two foreign-born parents, younger age, living in highly/extremely urban areas and having a lower income, lower education level and low medical risk for severe COVID-19 were risk factors for being unvaccinated in all populations. Substantial differences in the (strength of) determinants and population attributable fractions between populations were also observed. Socioeconomic status only partially mediated the association with being a migrant with two foreign-born parents. These findings illustrate that interventions targeting specific ethnic minority and migrant populations need further study with the aim to optimize the impact of vaccination programmes and improve health equity. To understand reasons behind non-uptake and design (community-based) interventions, qualitative and survey-based research is needed.