Background: Indoor air quality in schools is an important environmental health concern because children spend a substantial proportion of their time in classrooms and are particularly vulnerable to air pollutants. Objective: To assess common chemical, and biological pollutants in the indoor air of general education schools in Ulaanbaatar. Methods: A cross-sectional study was conducted from October 10, 2025, to March 1, 2026, in 16 purposively selected schools and 32 classrooms across six districts of Ulaanbaatar. PM2.5, PM10, CO₂, and microclimatic parameters were monitored continuously for seven days. Volatile organic compounds, formaldehyde, BTEX compounds, and radon were also measured. Airborne microorganisms were assessed using 160 air samples, and 160 surface swabs were collected. Results were compared with MNS 7106:2026, MNS 5484:2005, and MNS 6410:2018 standards. Results: The mean 24-hour concentrations of PM2.5 and PM10 were 25.2 and 36.1 µg/m³, respectively. PM2.5 exceeded the permissible level during winter and in schools located in apartment areas, whereas the mean PM10 concentration met the acceptable level. Total bacteria were detected in all air samples, with a mean concentration of 1,733.25 CFU/m³. Mould and fungi were detected in 56.3% of classrooms, and enteric bacteria were detected in 4.3% of surface swabs. Radon levels remained below the permissible limit, and pathogenic bacteria were not detected. Formaldehyde was detected in all samples, while total VOCs and toluene were detected in 81.3%; their mean concentrations remained within acceptable levels. In one classroom, the concentration of benzene was detected approximately 30 times higher the permissible level. Conclusion Although some indoor air-quality indicators met the relevant standards, PM2.5, total bacteria, mould and fungi, surface enteric bacteria, and benzene contamination require improvement and may pose health risks to children. Regular ventilation, improved cleaning and hygiene, proper maintenance of HEPA devices, and routine monitoring of particulate matter, mould, and VOCs are needed.