The density, form, and dimensions of urban morphology are important for healthy living conditions in cities, especially if they are related to the climate and air pollution. Morphology and environmental conditions determine the relationship between open and built space, the width of street spaces, the aerodynamic characteristics of wind currents, albedo, and the retention of pollutants, as well as determining the radiative exchange with the atmosphere. Studies on the COVID-19 pandemic have focused on the assumption of a possible relationship between the spread of the SARS-CoV-2 virus and the presence and concentration of airborne particulate matter (PM10 and PM2.5). This paper focuses on the research of indoor air quality (IAQ) in two schools with naturally ventilated classrooms in Ljubljana, Slovenia. The presence of particulate matter (PM2.5 and PM10) and the concentration of CO2 were studied, along with other microclimatic conditions, e.g., ambient temperature, relative humidity, air pressure, and wind conditions. These were compared and assessed via analysis of variance (ANOVA) and Duncan’s post hoc test. The main concern was to see how effective different ventilation strategies are, as well as how the openings in the classroom impact the concentrations of CO2 relative to the concentrations of PM2.5 and PM10 particles as a side effect of these ventilation strategies. The inconsistent application of recommended COVID-19 ventilation strategies suggests that IAQ in naturally ventilated classrooms is highly determined by individual perceptions of indoor air quality. The results also suggest that the IAQ is significantly affected by the schools’ urban environment; however, this is not considered within the national COVID-19 ventilation recommendations. Future ventilation guidelines for pandemics should also include the urban environment as a risk factor for inadequate IAQ, instead of focusing solely on pathogen characteristics.