<p><i>Alternaria</i> is an allergenic fungus that releases airborne spores, causing allergy and asthma in humans. The fungal spore contains twelve 11–58&#xa0;kDa allergens. The allergy threshold level of airborne <i>Alternaria</i> spores is 100/m³. This study examined temporal changes in the <i>Alternaria</i> spore season over 20 years and its correlation with air pollutants and meteorological factors. <i>Alternaria</i> spores’ historical dataset and meteorological factors from 2004 to 2023 were obtained from the Pakistan Meteorological Department. A dataset of ten air pollutants was recorded in Islamabad during 2022-23, standardized, and monthly averages were calculated. Airborne spore concentrations, meteorological factors, and air pollutants were statistically analyzed. The onset and end of the <i>Alternaria</i> spore season occurred in March and October. Seasonal spore integrals were highest in April to October and lowest in November to March. The dominant wind direction was southwest. The airborne <i>Alternaria</i> spore concentrations/m³ positively correlated with temperature and CO₂, and negatively correlated with relative humidity. The study concludes that the <i>Alternaria</i> spore season shifted between 2004 and 2023, which correlates with changes in meteorological factors and air pollutants. Findings of these investigations can be utilized by researchers, aerobiologists, clinicians, and the public to study airborne fungal spores’ temporal changes and allergies.</p>