Organic systems depend on intensive tillage for weed management, yet interest in conservation tillage methods is expanding in response to concerns regarding soil quality and environmental health. Deep zone tillage is one method that minimizes the width of soil disturbance to the planting row while providing sufficient disturbance to increase drainage and aeration and decrease compaction. This research addresses two constraints to an organic reduced tillage vegetable system: in-row weed control and fertility management. Two cover crop mixes, hairy vetch-rye or oats-peas were sown on two different dates at two different rates for the 2009 and 2010 growing seasons. Oat-pea cover crops were winter killed (leaving minimal residue) and hairy vetch-rye plots were flail mowed. Plots were then deep zone tilled, without incorporating cover crop biomass. Peppers were transplanted, and cover crop biomass in half the hairy vetch-rye plots was moved in-row to concentrate it, providing in-row weed control. Time required for cultivation and weeding by hand was recorded for economic analysis. Weed counts and biomass, pepper plant biomass, soil temperature, and soil N were monitored over the season. Planting cover crops earlier increased cover crop biomass significantly in 2009 but increasing seeding rates did not increase biomass either year. In-row mulch effectively decreased mid-season weed biomass. Hairy vetch-rye residue decreased soil temperatures both years, decreasing pepper plant size in these plots. All hairy vetch-rye plots had lower mid-season soil soluble N concentrations than oat-pea plots in 2009, and potentially mineralizable N did not differ either year. Despite the difference in pepper plant sizes throughout the season, total marketable fruit yields did not differ significantly between treatments in 2009 and oat-pea plots produced greater pepper yields than hairy vetch-rye plots in 2010. Partial enterprise budgets were calculated to compare the cost of weed control among treatments and oat-pea plots were found to be more cost effective both years due to greater pepper yield and reduced cover crop management costs and concentrating hairy vetch-rye residue was more cost effective than leaving it in place.