Negative short-term impact of logging on great ape distribution has been investigated but very little information is available on the long-term impacts of selective logging and management plans on ape habitats at a broader scale. We carried out a habitat suitability analysis using the presence data of great apes to identify the spatial relationships between their locations, logging activities patterns, and other human impacts (due to activities in rural communities) in an FSC-certified forestry concession (388,949 ha) in Cameroon. First, field data showed that the two great ape species, gorilla (Gorilla gorilla gorilla) and chimpanzee (Pan troglodytes troglodytes), did not differ in habitat type selection and they particularly appreciated highly dense rainforests which also lie within selectively logged zones. Second, we used MAXENT software to relate ape presence data to a set of predictor variables which represent environmental conditions and human disturbance factors (poaching, farming, trees felled to collect honey, logging roads). The model predicted that half of the whole concession may be suitable for the two primate species. Disturbances stemming from rural communities mainly correspond to poaching in the framework or not of usage rights. Road density was the strongest predictor of habitat choice by the great apes. Whereas the great apes tend to avoid zones with high road density, their population abundance increases in areas with a certain level of old logging roads. The vast majority of the predicted suitable habitats corresponds to areas logged less than 17 years ago (46.8% of the whole suitable area) where sustainable management practices have begun to be implemented, and unlogged areas (34.30%). Unsuitable habitats were mostly located in areas exploited before 2003 (45.46% of the unsuitable zones) with no reduced-impact logging practices, and in unlogged forests (41.51%). Our findings tend to confirm that selective logging combined with reduced-impact logging techniques which were more prevalent in FSC-certified concessions, may maintain or increase the spatial distribution of great ape habitats.