The effect of timber cutting and related management on species composition and diversity in tropical forests has been reported in earlier studies, but the potentially different effects on understory and canopy tree species remains unclear. Our study aim was to assess the variation in species composition and diversity of understory and canopy species along a timber removal (“logging”) gradient. We assessed the species composition, alpha and beta diversity, and compared species composition of canopy trees in plots with different management histories in Budongo. Our findings revealed logging contributed 18.1% to the beta diversity of species composition as measured by distance-based redundancy analysis (dbRDA) and species composition decreased with logging intensity (R2 = −0.415). Unlogged forest had higher species diversity for both understory and canopy tree species compared with logged forests. Species composition of logged/unlogged forests were significantly different from those of the forest succession types. Our study adds new information on the effect of logging on the species composition of understory and canopy trees in lowland tropical forests. We found logged forests do not recover species composition within seven decades, diversity within, and what previously distinct successional types were, have become, and remain, mixed in nature.