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The Mediterranean region is a climate change hotspot due to projected precipitation decreases, soil erosion, and rising temperatures in the coming decades. In such a context, wheat productivity is expected to decrease; thus, all available croplands will need to be farmed to meet food demands. It is therefore crucial to have adequate management to help balance wheat production and environmental protection in specific target environments. With this aim, we present a study in Castile and Leon (Spain) in which we assess conventional and certified organic wheat grain yield and quality. Moreover, we spatially define wheat cultivation suitability categories and monitor crop rotation practices. For wheat suitability mapping, a fuzzy interference system was used to standardize topographic (height and slope), edaphic (pH, soil erosion, organic matter, and texture), and climatic (rainfall and temperature) variables and create marginal, suitable, and very suitable wheat cultivation suitability categories. We calculated the area of wheat suitability categories with confidence intervals and discussed factors affecting productivity. Additionally, we assessed the performance of certified organic and conventionally managed fields with organic and chemical fertilization. We also examined crop rotations using Sentinel-2 data over two seasons (2020−21). Certified organic management yielded 50% less than conventional management in similar environments while maintaining grain quality. Besides management, the main causes of the yield gap are the growing environment and variety. In conventional wheat management, organic fertilization achieves comparable yields to chemical fertilization. Crop rotation practices are uncommon, and over 50% of fields rotate wheat-to-barley or wheat-to-wheat, indicating poor soil management. The region has 25% of cropland classified as marginal wheat croplands (163,503 ± 33,796 ha) producing <2500 kg/ha. Wheat organic agriculture has decreased yield gaps in marginal croplands compared to more productive areas. By farming organic wheat in marginal croplands, the best croplands might be used for more productive farming. • The studied region in Spain has 25% of cropland classified as marginal wheat croplands. • A fuzzy interference system has proven effective to decipher wheat suitability classes. • Sentinel-2 data allowed monitoring the uncommon crop rotation practices in the region. • Certified organic management yielded 50% less than conventional in similar settings. • Wheat organic agriculture has decreased yield gaps in marginal croplands. [ABSTRACT FROM AUTHOR]