The ecological effects of logging in the tropics have been analysed largely in terms of its impacts on species diversity and abundance. However, information is very limited regarding the impact of logging on ecological processes such as species interactions. Here we hypothesize that timber extraction per se, that is, in the absence of hunting, affects the abundance of the frugivorous spider monkey, Ateles geoffroyi, and that this has indirect effects on the recruitment of a predominant tree species, Manilkara zapota, and the diversity of the understorey plant community. We compared logged and unlogged sites, using a paired design. In each management condition we conducted line transects and interviews to evaluate spider monkey abundance and game preferences, respectively. Impact on plant recruitment and understorey diversity were evaluated using 2 × 2-m plots (N = 320) established under 40 M. zapota tree crowns. No spider monkeys were recorded in logged sites whereas they were abundant (15 ± 8 individuals per man-km) in unlogged sites. Interviews showed that spider monkeys are not hunted by local inhabitants. Logging was correlated with a reduction of the number of M. zapota fruits used by A. geoffroyi; an increase in the number of sites dominated by M. zapota; and a reduction in understorey plant diversity. Our results suggest that the absence of A. geoffroyi in logged sites can indirectly impact plant recruitment and diversity via the disruption of plant–frugivore interactions. Further work is needed to assess if these effects persist over the long term, to define if logging operations affect the overall diversity of tropical forests.