Cabo Verde was the first tropical archipelago colonized by Europeans. Historians have suggested that the first colonizers initiated archipelago-wide ecosystem degradation, loss of vegetation cover, and erosion. However, the human–environment interactions that led to the archipelago's current environmental status remain poorly understood. Here, we report the first palaeoecological study of past vegetation change and disturbance regimes for Cabo Verde. We present a 2130-yr old sediment sequence from a volcanic caldera (Cova de Paúl) located at ~1200 m asl on Santo Antão Island, for which we analyzed fossil pollen, non-pollen palynomorphs (NPPs), charcoal, silica bodies, and grain size distribution. Our analyses do not show evidence of the presence of temperate, tropical or subtropical forests growing on the summits of Santo Antão in pre-human times. The pollen record shows that scrubland and grasslands dominated the highlands and underwent compositional changes ca. 1850 and 1300 cal yr BP. These shifts overlap with erosion phases and are linked to intensified seasonality. Steady rates of sedimentation marked the period 1230 to ca. 350 cal yr BP, but an increase in charcoal concentrations indicate a drying phase. Increases in regional and local fire, peaks of coprophilous fungi and the presence of New World crop pollen (Zea mays) are interpreted as the onset of Portuguese settlement of the highlands after 450 BP. Sustained erosion between ca. 350 and 100 cal yr BP indicate soil degradation, and the pollen record shows the increase in introduced herbaceous taxa (Rosaceae, Centaurea, Verbenaceae) and exotic tree taxa (e.g. Pinus), while shifting abundances of coprophilous fungi indicate changes in land-use. The record shows stabilization of soils in the last century due to recent afforestation of the highlands. Further palaeoecological studies have the potential to provide further detail of the long-term dynamics of Cabo Verde ecosystems and to inform conservation initiatives.