question: Introduction Several studies in developed and developing countries have analyzed the health risk factors associated with coronavirus disease 2019 (COVID-19) mortality. Comorbid diseases are a key explanatory factor behind COVID-19 mortality, but current studies treat comorbidities in isolation, at average-population values, and rarely assess how death risk varies for different health profiles across institutions. Estimating death risk variations for different interactions between comorbid diseases and across healthcare institutions is crucial to gaining a significant depth of understanding in relation to mortality during the pandemic. Methods This study relies on data from approximately half a million people in Mexico (of all recorded cases through August 15, 2020) and on Bayesian estimation to provide a more robust estimate of the combined effect of several comorbidities and institutional inequalities upon COVID-19 mortality. Results The findings of the study illustrate the additive effects of several comorbid diseases with the presence of obesity, diabetes, hypertension, and CKD increasing the mortality risk of COVID-19. There are also variations in risk of death across the heterogeneous Mexican health system. Conclusions This study shows that COVID-19 mortality risk sharply increases in patients with 2 or more comorbid diseases (obesity, diabetes, hypertension, and cardiovascular diseases) in Mexico. However, death risk varied significantly across institutions for patients with the same comorbidity profile.