Objectives To investigate the prevalence, associated factors and socioeconomic inequalities in chronic disease relapses (CDR) during 2020 in Peru. Methods A secondary analysis was made of the National Household Survey on Living Conditions and Poverty (ENAHO) 2020. Participants older than 18 years who suffered from a chronic disease and with information about the occurrence of a CDR in the last 4 weeks prior to the survey were included. Adjusted prevalence ratios (aPRs) were estimated to determine the associated factors. Socioeconomic inequality in CDR was estimated using concentration curves (CC) and the Erreygers concentration index (ECI). Results Data from 38,662 participants were analyzed; the prevalence of CDR in the last 4 weeks prior to the survey was 16.5% (95% CI: 15.8-17.2). Being female (aPR 1.29; 95% CI: 1.21- 1.37), with regards to being male; being 30-39 (aPR 1.22; 95% CI: 1.05-1.42), 40-49 (aPR 1.29; 95% CI: 1.12-1.48), 50-59 (aPR 1.60; 95% CI: 1.41-1.82), and 60 years or older (aPR 1.80; 95% CI: 1.58-2.04), compared to 18-29; reaching up to primary (aPR 1.18; 95% CI: 1.07-1.31), or secondary education (aPR 1.13; 95% CI: 1.02-1.24), in contrast to tertiary education; presenting some physical, psychological or cognitive limitation (aPR 1.33; 95% CI: 1.21-1.46), with respect to experiencing no limitations; and being affiliated to a health insurance (aPR 1.18; CI 95%: 1.09-1.29), opposed to not having health insurance; were associated with a higher probability of CDR. Residing in the natural region of the coastal area (aPR 0.83; 95% CI: 0.74-0.92) was associated with a lower probability of relapse compared to residing in the jungle area. In people with limitations and residents of the jungle areas, the prevalence of CDR was concentrated in those with higher per capita spending. Conclusions Approximately 1 in 6 Peruvians with chronic diseases had a relapse within the last 4 weeks prior to the survey of 2020 and certain geographic and sociodemographic factors were found to be associated with CDR. It was also found that a higher concentration of CDR was observed in the population with the highest per capita spending with some limitations, as well as in residents of the jungle, implying the need for appropriate policy interventions that address CDR with a special focus on these populations.