Plant root systems are crucial in plant adaptation, exuding a wide array of compounds into the rhizosphere. The root exudate composition varies and may alter the metabolism of neighbouring plants. Characterizing root exudates in plants interacting with different neighbours presents challenges. We employed split-root systems for the application of differential treatments to parts of a single root system. We aimed to investigate how cover crops buckwheat and black oat modify their root exudates and root system architecture in response to inter- and intra-specific neighbours and assess the effects of these exudates on troublesome redroot pigweed. Non-targeted root exudate profiling revealed that neighbour presence induces systemic changes in root exudation, resulting in distinct responses depending on the neighbour’s identity. Root morphology analysis revealed that neighbouring plants could influence each other’s root architecture. The presence of redroot pigweed significantly decreased multiple root parameters in buckwheat, and vice-versa. Additionally, redroot pigweed root parameters were significantly reduced by the treatment of root exudates obtained from a cover crop-weed mixed culture. These findings provide insights into the understanding of how plants modify their root exudate composition in the presence of neighbours and how this impacts each other’s root systems.