The tropical African tree species Acacia nigrescens Oliv. was grown in environmentally controlled growth chambers at three CO2 concentrations representative of the Last Glacial Maximum (∼180 ppmv), the present day (∼380 ppmv), and likely mid-21st century (∼600 ppmv) CO2 concentrations. Isoprene (C5H8) emissions, per unit leaf area, were greater at lower-than-current CO2 levels and lower at higher-than-current CO2 levels relative to controls grown at 380 ppmv CO2. Changes in substrate availability and isoprene synthase (IspS) activity were identified as the mechanisms behind the observed leaf-level emission response. In contrast, canopy-scale emissions remained unaltered between the treatments as changes in leaf-level emissions were offset by changes in biomass and leaf area. Substrate concentration and IspS activity-CO2 responses were used in a biochemical model, coupled to existing isoprene emission algorithms, to model isoprene emissions from A. nigrescens grown for over 2 years at three different CO2 concentrations. The addition of the biochemical model allowed for the use of emission factors measured under present day CO2 concentrations across all three CO2 treatments. When isoprene emissions were measured from A. nigrescens in response to instantaneous changes in CO2 concentration, the biochemical model satisfactorily represented the observed response. Therefore, the effect of changes in atmospheric CO2 concentration on isoprene emission at any timescale can be modelled and predicted.