Further progress in reducing biodiversity loss relies on the improved quantification of the connections between drivers of habitat loss and subsequent biodiversity impacts. To this end, biodiversity impact metrics should be able to report linked trends in specific human activities and changes in biodiversity state, accounting for both the ecology of different species and the cumulative effects of historical habitat losses. These characteristics are not currently captured within a single metric. Here, we develop a globally applicable methodological framework that uses freely and publicly available datasets to quantify the relative impacts of anthropogenic activities on biodiversity. We use species-specific habitat suitability models to link specific land uses to ensuing changes in the likelihood that local populations of those species will persist. To illustrate our approach, we assess the impacts of soy expansion and other land uses within the Brazilian Cerrado on over 2,000 species of amphibians, birds, mammals and plants for three periods between 2000 and 2014. Our results showed that mammals and plants suffered the greatest overall reduction of suitable habitat. However, among endemic and near-endemic species—which face greatest risk of global extinction from habitat conversion in the Cerrado—birds and mammals were the most affected groups. While conversion of natural vegetation to grassland and planted pastures were together responsible for most of the biodiversity impact of recent changes, soy expansion (via direct conversion of natural vegetation) had the greatest impact per unit area. The total biodiversity impact of recent land-use change was concentrated in the southern states of the Cerrado—Minas Geráis, Goiás and Mato Grosso—but the impact on biodiversity of production of soy was greatest within the agricultural frontiers of Bahía and Piauí. The flexibility of our approach to examine linkages between biodiversity loss and specific human activities has clear potential to better characterize the pathways by which habitat loss drivers operate. Its capacity to incorporate species-specific ecological needs, through a globally applicable methodology, can improve the tangibility of biodiversity loss assessments.