Background: Diabetes mellitus (DM) is known to be more prevalent among migrants compared to their host populations. It is unclear whether DM prevalence differs between generations among migrants. We investigated the differences in DM prevalence among three generations of Moluccans, who have been living for over 65 years in the Netherlands, compared to the Dutch population. Methods: In this cross-sectional study, data of a healthcare insurance database on hospital and medication use (Achmea Health Database) were used. The dataset contained 5394 Moluccans and 52,880 Dutch persons of all ages. DM differences were assessed by means of logistic regression, adjusting for age, sex, urbanization, and area socio-economic status. Results: The prevalence of DM was higher in all generations of Moluccans compared to the Dutch. The adjusted odds ratios (AORs) for DM were significantly higher in total group of Moluccans compared to the Dutch (AOR 1.60, 95% CI 1.42–1.80) and across the first and second generation of Moluccans compared to the Dutch (first generation (1.73, 1.47–2.04) and second generation (1.44, 1.19–1.75). Higher AOR were found for first generation men (1.55, 1.22–1.97) and first (1.90, 1.52–2.37) and second (1.63, 1.24–2.13) generation Moluccan women compared to the Dutch. AOR for the third generation Moluccans was increased to a similar extent (1.51, 0.97–2.34), although not statistical significant. Conclusions: Our findings show higher odds of DM across generations of Moluccans compared to the Dutch. DM prevention strategies for minorities should be targeted at all migrant generations in host countries.