Abstract Background This study aimed to investigate the association between exposure to diverse indoor microbial aerosols and lower respiratory tract infections (LRTI) among children aged 1 to 59 months in Ibadan, Nigeria. Methods One hundred and seventy-eight (178) hospital-based LRTI cases among under-five children were matched for age (± 3 months), sex and geographical location with 180 community-based controls (under-five children without LRTI). Following consent from caregivers of eligible participants, a child’s health questionnaire, clinical proforma and standardized home-walkthrough checklist were used to collect data. Participant homes were visited and sampled for indoor microbial exposures using active sampling approach by Anderson sampler. Indoor microbial count (IMC), total bacterial count (TBC), and total fungal count (TFC) were estimated and dichotomized into high (> median) and low (≤ median) exposures. Alpha diversity measures including richness (R), Shannon (H) and Simpson (D) indices were also estimated. Conditional logistic regression models were used to test association between exposure to indoor microbial aerosols and LRTI risk among under-five children. Results Significantly higher bacterial and fungal diversities were found in homes of cases (R = 3.00; H = 1.04; D = 2.67 and R = 2.56; H = 0.82; D = 2.33) than homes of controls (R = 2.00; H = 0.64; D = 1.80 and R = 1.89; H = 0.55; D = 1.88) p < 0.001, respectively. In the multivariate models, higher categories of exposure to IMC (aOR = 2.67, 95% CI 1.44–4.97), TBC (aOR = 2.51, 95% CI 1.36–4.65), TFC (aOR = 2.75, 95% CI 1.54–4.89), bacterial diversity (aOR = 1.87, 95% CI 1.08–3.24) and fungal diversity (aOR = 3.00, 95% CI 1.55–5.79) were independently associated with LRTI risk among under-five children. Conclusions This study suggests an increased risk of LRTI when children under the age of five years are exposed to high levels of indoor microbial aerosols.