Weed management strategies differ in their ability to control weeds, and often have unique agroecological implications. To provide growers with an improved sense of trade-offs between weed control and ecological effects, we implemented several prominent organic weed management strategies in yellow onion in 2014 and 2015. Strategies included cultivation of weed seedlings during the early, weed-sensitive “critical period” of the crop; frequent cultivation events to ensure “zero seed rain”; and weed suppression with polyethylene or natural mulches. As expected, end-of-season weed biomass and weed seed production were greatest in the critical period system and nearly zero for the zero seed rain system. Weeds were also well controlled in natural mulch systems. Average onion yield per treatment was 50.7 Mg ha−1. In 2014, the critical period system and the polyethylene mulch systems demonstrated yield loss, likely due to weed competition and excessive soil temperature, respectively. Onion soluble solids content was also diminished in these systems in 2014, but bulb firmness was greatest in unmulched systems. Carabid beetles, earthworms, soil compaction, soil nitrate, and microbial biomass were affected by weed management strategy, with natural-mulched systems generally performing most favorably. However, these effects were not substantial enough to affect yield of a subsequent sweet corn crop grown in weed-free conditions. In contrast, sweet corn managed with only early-season cultivations demonstrated yield loss (P=0.004) in plots where the critical period treatment was implemented the prior year, indicating that weed competition resulting from abundant weed seed production in that system was the most influential legacy effect of the weed management strategies.