Weed management is challenging for vegetable crops highly sensitive to weed competition, such as onions. Thrips (Thysanoptera: Thripidae) are major insect pests of onion, causing damage through feeding, and vector bacterial pathogens causing rot. Both thrips and their associated pathogens are known to survive on many weed species in onion growing regions. Combining weeding with bio-pesticides may synergistically manage thrips and disease by reducing disease prevalence and indirectly increasing onion yield. However, disturbances from weeding may negatively impact natural enemies. We estimate the effects of organic weed management and bio-pesticides on weed density, thrips and natural enemy activity, disease severity, and yield. The experiment was a randomized complete block design, with four replications of each weeding (control, tine-weeded 2x, tine-weeded 4x, and hand-weeded) and bio-pesticide (control, OxiDate 2.0, Serenade) combination. Arthropods were monitored using yellow sticky cards, and weed counts, marketable yield, and bulb rot prevalence were estimated. Hand-weeding resulted in the lowest weed density and thrips abundance. Additionally, hand-weeding produced 9x higher yield compared to all other treatments. Significant interactions were observed between tine-weeding and bio-pesticide treatments. Natural enemy abundance was slightly negatively impacted by weeding, dependent on year. DNA metabarcoding results show high parasitoid diversity in onion systems and strong reads for multiple genera containing important known biological control agents. Our study suggests hand-weeding is necessary in the southeast for maximum onion yield. Future research should focus on exploring the impact of management on natural enemy communities in onion systems at a large scale.