The perceived risk of pest resurgence upon transition from conventional to organic-based farming systems remains a critical obstacle to expanding organic vegetable production, particularly where chemical fumigants have provided soilborne pest and disease control. Microplots were used to study the effects of soil amendments and cropping sequences applied over a 2-year transitional period from conventional to organic tomato (Solanum lycopersicum) cultivation on the incidence of bacterial wilt caused by Ralstonia solanacearum, purple nutsedge (Cyperus rotundus) reproduction, root galling by Meloidogyne incognita, and soil nematode populations. A continuation of tomato monoculture during the transitional period resulted in a disease incidence of 33%, as compared with 9% in microplots that were rotated with sunn hemp (Crotalaria juncea) and Japanese millet (Echinochloa crusgalli var. frumentacea). The benefits of disease control from a crop rotation extended into to a second season of organic tomato cultivation season, where bacterial wilt declined from 40% in microplots with a tomato monoculture to 17% in plots with a crop rotation sequence. Combining applications of urban plant debris with a continued tomato monoculture increased the incidence of bacterial wilt to 60%. During the transition period, tomato plants following a cover crop regime also had significantly lower levels of root galling from root-knot nematode infection compared with plants in the continuous tomato monoculture. Nutsedge tuber production was significantly increased in plots amended with broiler litter but not urban plant debris. Compared with a continuous monoculture, the results illustrate the importance of a systems-based approach to implementing transitional organic practices that is cognizant of their interactive effects on resident soilborne disease, weed, and pest complexes.