Background and aims Cereal-legume intercropping (IC) is proposed to address the challenges of increasing yields and improving crop nutrient quality, crucial for food security and human health. This study aimed to characterize the impact of pea-wheat IC on grain ionome composition, and asses its potential relation with the abundance of Pseudomonas spp. and Enterobacterales in plant roots. Methods In a field experiment, four pea varieties were cultivated in sole- or intercropping with wheat in two different soil types. Grain ionome was analysed by mass spectrometry, while Pseudomonas spp. and Enterobacterales abundances were quantified by qPCR. Results Pea grains intercropped with wheat showed increased concentrations of Ca, Mg, and Mo in one soil type, and higher Mn and Ni concentrations and total grain content in another. Wheat grains intercropped with peas, exhibited increased Cu, Fe, Mn, N, S, and Zn concentrations and/or total grain content, only in one soil type. Pseudomonas spp. showed increased abundance in pea root tissues when intercropped with wheat, specifically in one soil type. Pseudomonas spp. appeared to affect K, Fe, and Zn concentrations or total content in pea grains, depending on the cropping system. Conclusion These findings suggest that IC can enhance specific element concentrations and/or total grain content in pea and wheat grains, upon soil type. Pseudomonas spp. may facilitate nutrient uptake and translocation to grains. Further research is needed to understand the mechanisms behind element accumulation in IC grains and to explore the potential benefits of IC for plant nutrition and growth.