Screening suitable allelopathic crops and crop genotypes that are competitive with weeds can be a sustainable weed control strategy to reduce the massive use of herbicides. In this study, three accessions of common buckwheat Fagopyrum esculentum Moench. (Gema, Kora, and Eva) and one of Tartary buckwheat Fagopyrum tataricum Gaertn. (PI481671) were screened against the germination and growth of the herbicide-resistant weeds Lolium rigidum Gaud. and Portulaca oleracea L. The chemical profile of the four buckwheat accessions was characterised in their shoots, roots, and root exudates in order to know more about their ability to sustainably manage weeds and the relation of this ability with the polyphenol accumulation and exudation from buckwheat plants. Our results show that different buckwheat genotypes may have different capacities to produce and exude several types of specialized metabolites, which lead to a wide range of allelopathic and defence functions in the agroecosystem to sustainably manage the growing weeds in their vicinity. The ability of the different buckwheat accessions to suppress weeds was accession-dependent without differences between species, as the common (Eva, Gema, and Kora) and Tartary (PI481671) accessions did not show any species-dependent pattern in their ability to control the germination and growth of the target weeds. Finally, Gema appeared to be the most promising accession to be evaluated in organic farming due to its capacity to sustainably control target weeds while stimulating the root growth of buckwheat plants.