Organic wheat production systems have lower yields compared with intensive conventional production and often do not achieve the grain protein content and quality thresholds set by millers and bakers. In contrast, organic production methods were reported to result in higher concentrations of nutritionally desirable micronutrients and lower concentrations of the toxic metal Cd in wheat grain and wholegrain flour. However, although N-availability and variety characteristics are known to affect both gain yields and bread-making quality, the exact reasons for the yield gap and differences in grain processing and nutritional quality between organic and conventional spring wheat production in the UK are poorly understood. The overall aim of this study was therefore to determine to what extent changes in variety choice and fertilization regimes may reduce the yield gap and improve processing quality without affecting nutritional quality in organic spring wheat production. To achieve this aim, we compared crop health, yield, grain processing, and nutritional quality parameters in spring wheat produced using (i) six contrasting spring wheat varieties grown with a standard fertilization regime and (ii) one variety widely used by organic farmers (Paragon) with nine different fertilization regimes in (iii) three UK sites/farms with contrasting pedoclimatic conditions. Significant differences in foliar disease severity, grain yield, and quality parameters were detected between six contrasting spring wheat varieties when grown under organic management regimes. Specifically, the varieties Paragon and Tybalt were identified as the best-performing varieties with respect to foliar disease resistance and grain yield under organic farming conditions and also produced high processing and nutritional quality across the three UK sites. However, the highest grain yields were obtained by Paragon at the Gilchester site and Tybalt at the Sheepdrove and Courtyard sites, while the highest protein contents were produced by Tybalt at the Gilchester site and Paragon at the Sheepdrove and Courtyard sites, which suggests that there is a need for site-specific wheat variety selection in the UK organic sector. Although organic fertilizer input type and level also affected wheat performance, differences between fertilization regimes were smaller than those observed between the five contrasting varieties, which suggests that improvements in spring wheat breeding/selection have a greater potential for increasing crop yield and quality in the organic sector compared with changes to fertilization practices. Overall, results suggest it is feasible to breed/select spring wheat varieties that combine high protein, vitamin E, and micronutrients with low toxic metal (Cd, Pb) concentrations when produced under organic farming conditions. These findings also support the hypothesis that differences in variety choice by organic and conventional farmers have contributed to the differences in nutritional quality between organic and conventional wheat products reported in previous studies.