Allelochemicals cause yield differences under various ecosystems worldwide. Studies were conducted at the National Crops Resources Research Institute, Namulonge, Uganda during 2016 to investigate allelopathic properties of bioactive compounds in upland rice (NERICA 1), Desmodium uncinatum, Zea mays (LONGE 6H) and Mucuna pruriens root leachates. Studies involved pot screening, equal compartment agar experiments, germination tests and growth of potted plants. Results under the pot study indicated that maize, rice and mucuna leachates significantly (P ≤ 0.05), reduced root lengths (49%-63%), plant heights (48%-66%) and biomass (63%-75%) for Ageratum conyzoides, Bidens pilosa and Gallinsoga. parviflora weeds. G. parviflora root growth was reduced (20%-41%) and stem growth declined (19%-42%) when maize, rice and mucuna leachates were applied in the equal compartment agar study. Increased leachate concentrations (25%-75%) significantly (P ≤ 0.05), increased the mean germination time (0.4-2.8 days) for mucuna, desmodium, rice and maize as seed germination indices (SGI) were reduced (1.3%-49%). Potted mucuna, maize and desmodium reduced (1.3%-49%) rice root length. Potting mucuna with maize reduced (32%) mucuna leaf width while desmodium growth parameters were reduced (49%-64%) when potted with maize and mucuna. Potting maize with mucuna or desmodium increased the maize leaf length (18%) and SGI (25). Application of higher (25%-75%) rice/maize leachate concentrations similarly increased the maize leaf length (31%) and SGI (119). Allelopathic properties affect seed germination, crop growth and development, and characterise ecosystems age structures. Strategic management of crops under allelopathic ecosystems is critical.