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Abstract Climate extremes in tandem with biodiversity change affect plant emissions of biogenic volatile organic compounds, as a result, the formation of biogenic secondary organic aerosols. The resulting biogenic secondary organic aerosols can have a wide variety of impacts, such as on Earth’s radiative balance or cloud- and precipitation formation. However, at present, it is unclear how changing biodiversity will lead to changes in biogenic volatile organic compound emissions, biogenic secondary organic aerosols and their corresponding effects. We present a conceptual framework of the relationships between biodiversity and biogenic volatile organic compound emissions based on our current mechanistic understanding and combining knowledge from the fields of biology and atmospheric chemistry. Parts of this framework are tested in a case study using a tree diversity experiment. The relative differences in tree monocultures and mixtures show that the overall concentration of biogenic volatile organic compounds decreases with increasing biodiversity, but results for biogenic secondary organic aerosols are mixed and overall non-significant. A deeper understanding of how changing biodiversity influences biogenic organic compound emissions and biogenic secondary organic aerosol formation requires in-depth investigations of microclimate conditions, accurate monitoring of above- and below-ground biotic and abiotic stress, and manipulating stress conditions across long-term biodiversity experiments.