Primary biological aerosol particles (PBAPs) are major components of atmospheric aerosols that can influence human health, weather and climate processes. PBAPs have long been conceived to be mainly influenced by meteorological factors. Recently, oxidants and trace gases have been proven to transform bioaerosols in laboratory studies. However, it is still unknown about the relative importance of these two types of factors and their effects in real atmosphere. Here, we show that protein-like fluorescent biological aerosol particles (ProteinL-FBAP) measured by a Wideband Integrated Bioaerosol Sensor (WIBS-4A) accounted for 9.2% ± 4.8 % (average ± standard variation) of total particles by number (0.8–10 µm) in the urban atmosphere of Beijing in summer. Its temporal variation can be mainly predicted by NO2 and O3 rather than meteorological parameters (temperature, relative humidity and wind speed). With increasing concentration of NO2 throughout the whole day and O3 in the daytime, the number concentration of ProteinL-FBAP increased across the whole size range of 0.8–10 µm. Meantime, the size distribution of ProteinL-FBAP shifted to their smaller and larger size, respectively. Our results indicate the fragmentation of large bioaerosols (NO2 related) such as pollen grains and the accretion of substances to bioaerosols (O3 related), which demonstrate the importance of oxidants and trace gases on bioaerosols in the atmosphere.