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Background Gestational diabetes increases risk for type 2 diabetes seven-fold, creating a large public health burden in a young population. In the US, there are no large registries for tracking postpartum diabetes screening among women in under-resourced communities who face challenges with access to care after pregnancy. Existing data from Medicaid claims is limited as women often lose this coverage within months of delivery. In this study, we aim to leverage data from electronic health records and administrative claims to better assess postpartum diabetes screening rates among low income women. Methods A retrospective population of 1078 women with gestational diabetes who delivered between 1/1/2010 and 10/8/2015 was generated by linking electronic health record data from 21 Missouri Federally Qualified Health Centers (FQHCs) with Medicaid administrative claims. Screening rates for diabetes were calculated within 12 weeks and 1 year of delivery. Initial screening after the first postpartum year was also documented. Results Median age in the final population was 28 (IQR 24–33) years with over-representation of black non-Hispanic and urban women. In the final population, 9.7% of women had a recommended diabetes screening test within 12 weeks and 18.9% were screened within 1 year of delivery. An additional 125 women received recommended screening for the first time beyond 1 year postpartum. The percentage of women who had a postpartum visit (83.9%) and any glucose testing (40.6%) in the first year far exceeded the proportion of women with recommended screening tests. Conclusions Linking electronic health record and administrative claims data provides a more complete picture of healthcare follow-up among low income women after gestational diabetes. While screening rates are higher than reported with claims data alone, there are opportunities to improve adherence to screening guidelines in this population. Electronic supplementary material The online version of this article (10.1186/s12889-019-6475-0) contains supplementary material, which is available to authorized users.