BACKGROUND: Indoor smoke exposure is common in developing countries and may influence nasopharyngeal (NP) pneumococcal colonization density and risk of acute respiratory illness. We compared colonization density among Andean children living in households previously enrolled in a randomized controlled trial of a home intervention package including improved stoves to reduce smoke, kitchen sinks, and water disinfection. METHODS: We enrolled 260 children aged <3 years and made weekly household visits to assess for acute respiratory illness (ARI) and collect nasal swabs for respiratory virus polymerase chain reaction (PCR) testing during ARI. At monthly intervals, NP swabs were collected to determine pneumococcal colonization density through quantitative lytA PCR. We used linear quantile mixed-effects models to compare median log-transformed colonization densities among children in households randomized to the control (n = 129) versus intervention (n = 131) in sequential time points, accounting for random effects of multiple samples from individual children. Other covariates included age, sex, month, antibiotic exposure, and timing of sample collection relative to ARI with and without viral detection. RESULTS: Age and sociodemographic characteristics were similar between groups. Although no differences were observed in densities between groups, colonization density varied significantly over time in both groups, with highest densities coinciding with spring months. Time during and after virus-associated ARI was also associated with higher pneumococcal colonization density than time remote from ARIs. CONCLUSIONS: A home intervention package, including improved stoves, was not associated with changes in pneumococcal densities in young Andean children. However, increasing pneumococcal density was observed with spring season and viral-associated ARIs.