The estimated burden of chronic disease among people living with HIV (PLWH) varies considerably by data source, due to differences in case definitions, analytic approaches, and underlying patient populations. We evaluated the burden of diabetes (DM) and chronic kidney disease (CKD) in two large data systems that are commonly queried to evaluate health issues affecting HIV care patients: the Medical Monitoring Project (MMP), a nationally representative sample, and the Centers for AIDS Research Network of Integrated Clinical Systems (CNICS), a clinical cohort. In order to reconcile these two data sources, we addressed issues common to observational data, including selection bias, missing data, and development of case definitions. The overall adjusted estimated prevalence of DM and CKD in MMP was 12.7% and 7.6%, respectively, and the overall prevalence of DM and CKD in CNICS was 9.9% and 8.3%, respectively; prevalence estimates increased with age in both data sources. After reconciling the approach to analyzing MMP and CNICS data, sub-group specific prevalence estimates of DM and CKD was generally similar in both data sources. Both data sources suggest a considerable burden of disease among older adults in HIV care. MMP and CNICS can provide reliable data to monitor HIV co-morbidities in the US.