Increasing stable crop yields and nutrient quality are essential to ensure food security and promote human health. Cereal-legume intercropping (IC) has been proposed to meet these challenges since IC allows to reduce the use of nitrogen fertilizer, thanks to N uptake by the cereal promoted by the symbiosis between the legume and N-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 pea and wheat. The goals of the present study were to (i) characterize the impact of pea-wheat IC on the abundance of Pseudomonas spp. and Enterobacterales and (ii) assess a possible relation of their abundance with changes in grain ionome associated with IC. Four pea (Pisum sativum) varieties were cultivated in sole- or IC with wheat (Triticum aestivum) in clay and sandyloam-clay soil types. Bacterial abundances were assessed by qPCR, and grain ionome by mass spectrometry. Pseudomonas spp. were more abundant in pea, and Enterobacterales in wheat when cultivated in IC. Grain ionome was also impacted by IC with an increased content in Cu, Mn, Fe and S in wheat, and in Mn, Mo, and Ni in pea. A positive correlation was found between the Pseudomonas spp. abundance and the Mo content in pea grains. These results indicate that pea-wheat IC increases the abundance of bacterial groups and suggest that the increased occurrence of Pseudomonas spp. could contribute not only to Fe but also to Mo nutrition.