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With the continuing 20% growth rate in the organic industry, organic vegetable crop production has increased to 98,525 acres in the United States. The requirement for certified organic vegetable producers to implement a soil-building plan has led to the development of soil fertility systems based on combinations of organic fertilizers and cover crops. To determine optimal soil fertility combinations, conventional and organic bell pepper (Capsicum annuum) production was evaluated from 2001 to 2003 in Iowa, comparing combinations of two synthetic fertilizers and three compost-based organic fertilizers, and a cover crop treatment of hairy vetch (Vicia villosa) and rye (Secale cereale) in a strip-tilled or fully incorporated cover crop system. Organic pepper growth and yields equaled or surpassed conventional production when nitrogen (N) was provided at 56 or 112 kg·ha−1 from compost-based organic fertilizer. Soil analysis revealed higher N in plots where cover crops were tilled compared with strip-tilled plots, leading to recommendations for sidedressing N in strip-tilled organic pepper production. Increased incidence of disease was also detected in strip-tilled plots. Postharvest weight loss after 6 weeks in storage was similar in organic and conventional peppers. The addition of calcium and sulfur products in conventional or organic fertilizer regimes did not increase pepper production or postharvest storage potential. Despite application challenges, cover crops will remain as critical components of the organic farm plan for their soil-building benefits, but supplementation with approved N sources may be required for optimal pepper production. Organic growers should conduct their own tests of organic-compliant soil amendments to determine cost effectiveness and value for their site before large-scale application.