Intercropping is a farming practice that fights pests and diseases and improves plant growth. The use of plant growth-promoting rhizobacteria (PGPR) strains to boost the yield of intercrops constitutes a promising tool in agricultural practice. This study investigated the impact of single inoculation and co-inoculation with PGPR on plant biomass and phosphorus (P) and nitrogen (N) concentrations under different cropping systems. Two PGPR strains with different traits were selected: PGP13 (Rahnella aquatilis) and PS11 (Pseudomonas sp.). A greenhouse experiment was designed using durum wheat (Triticum durum L.) and faba bean (Vicia faba L.), sole cropped or intercropped, including four inoculation treatments: (i) uninoculated, (ii) inoculated with PS11 (iii) inoculated with PGP13, and (iv) co-inoculated with PS11 + PGP13. Co-inoculation under the intercropping system improved plant dry matter and enhanced bean pod and wheat spike weights to 685.83% and 385.83%, respectively, of the values for uninoculated, intercropped plants. Higher P and N concentrations were detected in intercropped, co-inoculated plants and in bean pods and wheat spikes. The results were then submitted to principal component analysis, showing that treatments with higher biomass and nutrient concentrations were strongly correlated with intercropped, co-inoculated plants.