Increasing stable crop yields and nutrient quality is essential to ensure food security and promote human health. Cereal-legume intercropping (IC) has been proposed to meet these challenges since IC reduces the need for nitrogen fertilizer, due to N uptake by the cereal, which is facilitated by the symbiotic relationship between the legume and nitrogen-fixing bacteria. Other bacterial groups, such as Pseudomonas spp., are known to promote pea nutrition in Fe, Mg and P, and Enterobacterales to impact Fe and P dynamic in both pea and wheat. The goals of the present study were to (i) characterize the impact of pea-wheat IC on the occurrence of Pseudomonas spp. and Enterobacterales and (ii) assess a possible relation between their occurrence and changes in grain ionome associated with IC. We cultivated four varieties of peas (Pisum sativum) either alone or in IC with wheat (Triticum aestivum) in clay and sandy-loam-clay soil types. Bacterial abundances were assessed by qPCR, and grain ionome by mass spectrometry. Pseudomonas spp. were more abundant in pea when cultivated in IC, while Enterobacterales in wheat. Furthermore, IC had a significant impact on the grain ionome, leading to increased levels of Cu, Mn, Fe and S in wheat, and in Mn, Mo, as well as of Ni in pea. These results indicate that pea-wheat IC increases the occurrence of bacterial groups. Moreover, positive correlations observed between bacterial occurrences and certain grain element content, suggesting that these bacterial groups may contribute to the increased element content in the grains of IC plants.