The harvest of non-timber forest products (NTFPs), together with other sources of anthropogenic disturbance, impact plant populations greatly. Despite this, conservation research on NTFPs typically focuses on harvest alone, ignoring possible confounding effects of other anthropogenic and ecological factors. Disentangling anthropogenic disturbances is critical in regions such as India's Western Ghats, a biodiversity hotspot with high human density. Identifying strategies that permit both use and conservation of resources is essential to preserving biodiversity while meeting local needs. We assessed the effects of NTFP harvesting (fruit harvest from canopy and lopping of branches for fruit) in combination with other common anthropogenic disturbances (cattle grazing, fire frequency and distance from village), in order to identify which stressors have greater effects on recruitment of three tropical dry forest fruit tree species. Specifically, we assessed the structure of 54 populations of Phyllanthus emblica, P. indofischeri and Terminalia chebula spread across the Nilgiri Biosphere Reserve, Western Ghats to ask: (1) How are populations recruiting? and (2) What anthropogenic disturbance and environmental factors, specifically forest type and elevation, are the most important predictors of recruitment status? We combined participatory research with an information-theoretic model-averaging approach to determine which factors most affect population structure and recruitment status. Our models illustrate that for T. chebula, high fire frequency and high fruit harvest intensity decreased the proportion of saplings, while lopping branches or stems to obtain fruit increased it. For Phyllanthus spp, recruitment was significantly lower in plots with more frequent fire. Indices of recruitment of both species were significantly higher for plots in more open-canopy environments of savanna woodlands than in dry forests. Our research illustrates an approach for identifying which factors are most important in limiting recruitment of NTFP populations and other plant species that may be in decline, in order to design effective management strategies.