Crop domestication has led to the development of distinct trait syndromes, a series of constrained plant trait trade‐offs to maximize yield in high‐input agricultural environments, and potentially constrained trait plasticity. Yet, with the ongoing transition to organic and diversified agroecosystems, which create more heterogeneous nutrient availability, this constrained plasticity, especially in root functional traits, may be undesirable for nutrient acquisition. Such agricultural systems require a nuanced understanding of the soil‐crop continuum under organic amendments and with intercropping, and the role crop genetic resources play in governing nutrient management and design. In this study, we use a functional traits lens to determine if crops with a range of domestication histories express different functional trait plasticity and how this expression changes with soil amendments and intercropping. We utilize a common garden experiment including five wheat (Triticum aestivum) varietals with a range of domestication histories planted in a factorial combination with amendment type (organic and inorganic) and cropping design (monoculture or intercropped with soybean). We use bivariate, multivariate and trait space analyses to quantify trait variation and plasticity in five leaf and five root functional traits. Almost all leaf and root traits varied among varieties. Yet, amendment type was nearly inconsequential for explaining trait expression across varieties. However, intercropping was linked to significant differences in root acquisitive strategies, regardless of the varietals' distinct history. Our findings show substantial leaf and root trait plasticity, with roots expressing greater trait space occupation with domestication, but also the strong role of management in crop trait expression. We underscore the utility of a functional trait‐based approach to understand plant–soil dynamics with organic amendments, as well as the role of crop genetic histories in the successful transition to low‐input and diversified agroecosystems.