Objective: To compare excess mortality by district quintiles according to the Human Development Index (HDI) in Metropolitan Lima, the capital of Peru, and analyze the socioeconomic factors associated with excess mortality within the context of COVID-19. Methods: Retrospective cross-sectional analysis of the mortality records from non-violent causes registered in the National Death Information System in the 50 districts of Metropolitan Lima of the first 24 weeks of the years 2019 and 2020. Descriptive analysis was performed using contingency tables and time series graphs by sex, age group, and quintile of the district of residence according to the HDI. Negative binomial regression analysis was performed to identify possible explanatory factors for excess mortality. Results: An excess of 20 093 non-violent deaths and 2,979 confirmed deaths from COVID-19 were registered in Metropolitan Lima during the study period. The increase was observed primarily in men and adults aged 60 and over. Residents in the districts belonging to the fifth quintile, according to HDI, presented, in most cases, the lowest rates. Multivariate analysis revealed that a higher HDI level (p = 0.009) and a higher proportion of inhabitants living in extreme poverty (p = 0.014) decreased the excess mortality. Conclusion: Excess of non-violent deaths in Metropolitan Lima is higher in the quintiles with the lowest HDI, in men, and the age group from 60 to more years of age. The study of social and economic health determinants in Peru is crucial for the design of measures to be taken by the government against the COVID-19 pandemic.