There is a gap in the epidemiological data on obesity and COVID-19 mortality in low and middle-income countries worst affected by the COVID-19 pandemic, including Peru. In this ecological study, we explored the association between body mass index (BMI), the prevalence of overweight and obesity, and the COVID-19 mortality rates in 25 Peruvian regions, adjusted for confounding factors (mean age in the region, mean income, gender balance and number of Intensive Care Unit (ICU) beds) using multiple linear regression. We retrieved secondary region-level data on the BMI average and prevalence rates of overweight and obesity in individuals aged ≥ 15 years old, from the Peruvian National Demographics and Health Survey (ENDES 2020). COVID-19 death statistics were obtained from the National System of Deaths (SINADEF) from the Peruvian Ministry of Health and were accurate as of 3 June 2021. COVID-19 mortality rates (per 100,000 habitants) were calculated among those aged ≥ 15 years old. During the study period, a total of 190,046 COVID-19 deaths were registered in individuals aged ≥ 15 years in 25 Peruvian regions. There was association between the BMI (r = 0.74; p = 0.00001) and obesity (r = 0.76; p = 0.00001), and the COVID-19 mortality rate. Adjusted for confounding factors, only the prevalence rate of obesity was associated with COVID-19 mortality rate (β = 0.585; p = 0.033). These findings suggest that as obesity prevalence increases, the COVID-19 mortality rates increase in the Peruvian population ≥ 15 years. These findings can help to elucidate the high COVID-19 mortality rates in Peru.