Forest loss has been pointed out as the main cause for the dramatic reduction of chimpanzee populations in West Africa, namely in Guinea-Bissau, where Pan troglodytes verus is currently restricted to the southern coastal areas. Thus, conservation of this species depends on the protection of the remaining suitable forests, on the integrity of the landscape mosaics that include them, and on the connectivity between forest patches. The aim of this study was to develop a model that predicts habitat suitability for chimpanzee under different land cover scenarios, and that supports a multi-temporal analysis of the recent habitat evolution in southern Guinea-Bissau. Field data of P. t. verus were combined with multi-temporal satellite imagery (1986, 1994 and 2003) in a GIS to build, validate and apply a model that predicts habitat suitability in the Cantanhez region. An ensemble of seven modelling techniques was used to derive habitat suitability maps. Results show that suitable habitats for chimpanzees are closely related to the presence of forest, and that landscape-level features (composition, structure and function) are important factors influencing chimpanzee distribution. Multi-temporal analysis of habitat suitability suggests a contraction of suitable areas during the studied period, mostly due to forest loss in the Cantanhez region. The proposed framework provides a useful tool to support conservation planning and the design of management strategies for chimpanzee populations in West Africa, and can be extended to other regions and species facing similar pressures.