Cover crops with reduced tillage technology (CC-RT) can foster soil health and functioning, a crucial agroecological principle in any transition strategy to more sustainable agricultural systems. However, CC-RT commonly strongly relies on herbicides and synthetic fertilizers, and vegetable crop yields are variable and often low. We assessed the effects of two tillage systems (RT and conventional tillage) and the application of native effective microorganisms (NEM) on onion crop growth and development, yield, N-status, weed pressure, and soil physico-chemical and biological quality after a summer CC, without using herbicides or synthetic fertilizers. Using a participatory research strategy, we conducted a two-year experiment at an experimental station and a one-year trial on two commercial farms. Onion yields were generally low (between 10 and 16 Mg ha−1) and lower in 2019 than in 2020, and lower in RT than in CT in 2020. The relatively low yields in 2019 and RT were associated with poor crop growth and development and leaf-N concentrations below the critical threshold in the early stages of crop development. Soil bulk density was not limiting crop growth in any treatment. Soil mineral N was lower in 2019 than in 2020 and did not significantly differ between treatments. Soil biological activity was higher in RT than in CT. Although the CC residue soil cover in the early stages of the onion crop in RT was more than 50%, RT had a higher weed pressure than CT, which was reversed later in the growing season. The NEM application did not significantly affect most crop, weed, and soil variables. In conclusion, a reduced tillage system for onions without herbicides and synthetic fertilizers is within reach. However, further research is needed to manage weeds and soil N supply dynamics to make CC-RT feasible for no or low agrochemical input systems.