Patient-centered medical homes (PCMH) are primary care delivery models that improve care access and population-level health outcomes, yet they have not been observed to narrow racial-ethnic disparities in the Veteran Health Administration (VHA) or other health systems. We aimed to identify and compare underlying drivers of persistent hypertension and diabetes control differences between non-Hispanic Black (Black) and Hispanic versus non-Hispanic White (White) patients before and after PCMH implementation in the VHA. Among Black and Hispanic versus White VHA primary care patients in 2009 (nhypertension = 26,906; ndiabetes = 21,141) and 2014 (nhypertension = 83,809; ndiabetes = 38,887), we retrospectively examined hypertension control (blood pressure<140/90) and diabetes control (hemoglobin A1c <9) obtained through random chart abstraction of patient health records nationally via VHA's quality monitoring program. We fit linear probability regression models, adjusting for age, gender, comorbidity, and socioeconomic status (SES). Blinder-Oaxaca and Smith-Welch decomposition methods were used to parse out explained and unexplained contributors to health disparity between racial-ethnic groups pre- and post-PCMH implementation. Compared to White patients, hypertension and diabetes control remained significantly lower for Black (-6.2%[0.4%] and -3.1%[0.6%], respectively; p's<0.001) and Hispanic (-1.4%[0.8%] and -4.0%[1.0%], respectively; p's<0.001) patients following VHA PCMH implementation. Most racial-ethnic differences (55.7-92.3%; all p<0.05) were not attributed to age, gender, comorbidity, and SES. The contribution of explained versus unexplained factors did not significantly change over time. While many explanations for persistent racial-ethnic disparities in disease control among veterans exist, our study did not find that it was due to an influx of "sick" or "socioeconomically vulnerable" patients into the VHA following PCMH implementation. Instead, unexplained differences may be due to differential healthcare and community experiences (e.g., discrimination). Understanding underlying pathways leading to health disparities will better inform policy and clinical interventions to improve PCMH care delivery to racial-ethnic minority patients in health systems.