This study assessed changes in complete pneumococcal vaccination coverage (CPVC) among Peruvian children <5 years before and after the COVID 19 pandemic and evaluated regional differences, associated sociodemographic factors and wealth-related inequality. 2018–2023 Demographic and Health Surveys (DHS) was analyzed. CPVC was defined as receiving the full 2 + 1 schedule of the 13 valent pneumococcal vaccine. Children aged 13–60 months were included. Multivariable analysis used modified Poisson regression and wealth related inequality was assessed using the Concentration index and Erreygers’s corrected Concentration index at national and regional levels. Among 95,586 children, CPVC decreased from 71.9% in 2019 to 69.4% in 2020 (p = 0.003), then returned to pre Covid levels from 2021 onward (72.2% in 2023; p = 0.001), particularly in Lima Metropolitana. Puno (53.3–58.6%) and Madre de Dios (50.9–62.1%) consistently showed the lowest coverage. Nationally, wealth- or sociodemographic related inequalities were minimal; however, regional interactions indicated that the effect of wealth on CPVC varied by area. Depending on the region, factors such as age group, household members and mather’s education were associated with lower CPVC, whereas age at first pregnancy, institutional birth, antenatal care and access to information increased CPVC. Ucayali showed persistently higher CPVC among wealthier populations. Despite a temporary decline during the pandemic, CPVC in Peru rapidly recovered, although regional gaps persist.