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Weed community structure, including composition, taxonomic and functional diversity, may explain variability in crop quality, adding to the variability accounted by management, climatic and genetic factors. Focusing on Mediterranean rainfed wheat crops, we sampled weed communities from 26 fields in Spain that were either organically or conventionally managed. Weed communities were characterized by their abundance and taxonomic, compositional and trait-based measures. Grain protein concentration and the glutenin to gliadin ratio were used as indicators of wheat grain quality. Linear mixed effects models were used to analyze the relationship between crop quality and weed community variables, while accounting for environmental factors. Nitrogen fertilization, previous crop and precipitation explained a large portion of the variation in wheat grain protein concentration (R2marginal = 0.39) and composition (R2marginal = 0.26). Weed community measures had limited effects on grain quality (increasing R2marginal of models by 1% on average). The weed effects were related to the composition and the functional structure of their communities, but not to their abundance. Environmental conditions promoting higher protein concentration were also selecting for weed species with competitive attributes, whereas the role of weed functional diversity depended on the functional trait and on the resource limiting crop grain quality. Understanding the mechanisms of weed effects on crop quality could aid on designing sustainable weed management practices.