Studies on the ecological impacts of non-timber forest products (NTFP) harvest reveal that plants are often more resilient to fruit and seed harvest than to bark and root harvest. Several studies indicate that sustainable fruit harvesting limits can be set very high (>80% fruit harvesting intensity). For species with clonal and sexual reproduction, understanding how fruit harvest affects clonal reproduction can shed light on the genetic risks and sustainability of NTFP harvest. We studied 18 populations of a gallery forest tree, Pentadesma butyracea (Clusiaceae), to test the impact of fruits harvest, climate and habitat size (gallery forest width) on the frequency of sexual or clonal recruitment in Benin, West Africa. We sampled populations in two ecological regions (Sudanian and Sudano-Guinean) and in each region, we selected sites with low, moderate and high fruit harvesting intensities. These populations were selected in gallery forests with varying width to sample the natural variation in P. butyracea habitat size. Heavily harvested populations produced significantly less seedlings but had the highest density and proportion of clonal offspring. Our study suggests that for plant species with dual reproductive strategy (via seeds and clonal), fruit harvesting and associated disturbances that come with it can lead to an increase in the proportion of clonal offspring. This raises the issue that excessive fruit harvest by increasing the proportion of clonal offspring to the detriment of seed originated offspring may lead to a reduction in genetic diversity with consequence on harvested species capability to withstand environmental stochasticity.