The current study is aimed at elucidating the proteomic responses in the seed tissue of durum wheat Triticum aestivum L. (cultivar HD-3086) triggered by native (CP4) and non-native (AHP3) PGPB (Bacillus spp.) alone and in combination with AM fungi (Glomus fasciculatum + Gigaspora sp.) under field conditions. Our results suggest that application of CP4 and AHP3 (in combination with AM fungi) promote differential abundance of multiple regulatory seed storage and other proteins over untreated control. Thus, combined application of tripartite (CP4+AHP3+AMF) microbial consortia could offer a more sustainable approach to enhance crop yield in wheat.