Alley cropping systems can change the weed community composition and reduce common weed species. However, it is unclear how different woody species intercalated with corn can affect weed abundance and community structure and corn yield in the tropics. The present study examined weed species diversity and community composition in alley cropping systems with three woody species associated with corn: Leucaena leucocephala (Lam.) de Wit, Guazuma ulmifolia Lam., and Moringa oleifera Lam. independently, and corn monoculture, as a control. The tree most dominant weed species were Ruellia nudiflora (Engelm. & A. Gray) Urb., Cynodon dactylon (L.) Pers., and Portulaca pilosa L. Our results showed that the alley cropping system compared with corn monoculture reduced the densities of common abundant weed species, changed weed community composition, maintained or increased plant diversity, but did not affect grain yield (t/h). Based on the sample completeness profile we found that Leucaena associated with corn had a higher weed diversity of order q = 1 and 2 (Shannon and Simpson index) and showed higher evenness compared with corn monoculture, which showed the lowest evenness of all treatments. We found nine weed species that only grow in alley cropping systems and Waltheria americana L., Momordica charantia L. and Porophyllum punctatum (Mill) S.F. Blake. with higher densities. Our findings support the hypothesis that alley cropping systems not only changes weed community composition, but also favours biodiversity conservation without reducing corn yield.