Summary Milicia regia (Moraceae) is a dioecious light‐demanding (Pioneer) timber tree of West Africa. Experiments in shadehouses were used to examine the influence of light and soil source (beneath and away from conspecific adults) on mortality and growth of its seedlings in relation to fungal pathogens and arbuscular mycorrhizal (AM) colonization. The experiment in Ghana included treatments for light (2% and 20% of unshaded irradiance), three soil sources (under female, under male and 200 m distant from adults), and two different fungicide treatments. The results showed significant effects of irradiance, soil source and fungicide on both seedling mortality and accumulated biomass. Biomass was greater and mortality reduced at higher irradiance. Fungicide application reduced mortality in 2% irradiance, but had no significant effects at 20%, although AM infection of seedlings grown in soils from beneath adults was severely reduced. Mortality was greatest in soil from beneath female trees and least in soil distant from adult conspecifics. However, biomass in 20% irradiance was greater in soil from beneath females, possibly because of enhanced AM colonization: seedlings had a significantly higher percentage root length colonized by AM fungi beneath adult conspecifics, and biomass accumulation was significantly correlated with root length colonized by AM fungi. There were significant interactions amongst light, soil source and fungicide treatments that attest to the complexity of spatial effects on seedling establishment in tropical forest. Whilst there was clear evidence of pathogen‐mediated effects that provides support for Janzen‐Connell spacing mechanisms, and escape from the parent tree increases the chances of arriving in gaps, spatial differences in AM fungal communities may act in the opposite direction and enhance seedling growth close to adult conspecifics. The complexity of interactions between abiotic and biotic factors and the way in which these factors can vary spatially to affect seedling recruitment may be an important factor contributing to the maintenance of tree species diversity in tropical forests.