We include biodiversity impacts in forest management decision making by incorporating the countryside species area relationship model into the partial equilibrium model GLOBIOM-Forest. We tested three forest management intensities (low, medium, and high) and limited biodiversity loss via an additional constraint on regional species loss. We analyzed two scenarios for climate change mitigation. RCP1.9, the higher mitigation scenario, has more biodiversity loss than the reference RCP7.0, suggesting a trade-off between climate change mitigation, with increased bioenergy use, and biodiversity conservation in forests. This trade-off can be alleviated with biodiversity-conscious forest management by (1) shifting biomass production destined to bioenergy from forests to energy crops, (2) increasing areas under unmanaged secondary forest, (3) reducing forest management intensity, and (4) reallocating biomass production between and within regions. With these mechanisms, it is possible to reduce potential global biodiversity loss by 10% with minor changes in economic outcomes. The global aggregated reduction in biodiversity impacts does not imply that biodiversity impacts are reduced in each ecoregion. We exemplify how to connect an ecologic and an economic model to identify trade-offs, challenges, and possibilities for improved decisions. We acknowledge the limitations of this approach, especially of measuring and projecting biodiversity loss.