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Abstract To improve cover crops such as peas (Pisum sativum), as rotational partners, intraspecific variation for cover cropping traits such as nutrient mobilization, carbon deposition, and beneficial microbial recruitment must be identified. The majority of research on cover crops has focused on interspecies comparisons for cover cropping variation with minimal research investigating intraspecies variation. To address if variation of cover cropping traits is present within a cover cropping species, we grew 15 diverse accessions (four modern cultivars, three landraces, and eight wild accessions) of pea in a certified organic setting. We measured various cover cropping traits, such as nutrient mobilization, soil organic matter deposition, and microbial recruitment, and quantified the effect of pea accession on the growth and yield of a subsequently planted crop of corn (Zea mays). We discovered that the domestication history of pea has a significant impact on soil properties. Specifically, domesticated peas (modern cultivars and landraces) had higher average plant–soil feedback values for amounts of nitrogen, carbon, and manganese compared to wild peas. Additionally, no variation for prokaryotic recruitment (α‐ and β‐diversity) was observed within pea; however, we did observe significant variation for fungal recruitment (α‐ and β‐diversity) due to domestication and accession. Our results demonstrate that there is variation present in peas, and likely all crops, that can be selected to improve them as rotational partners to ultimately boost crop yields in sustainable agroecosystems.