Microbial populations have diverse roles within rhizosphere where interactions among distinct microorganisms along with the host may lead to mutualistic associations. The present study aimed to investigate the nutritional and antioxidant qualities of seeds and pericarp of pea raised from seeds treated with beneficial microbes namely Bacillus subtilis BHHU100, Trichoderma harzianum TNHU27 and Pseudomonas aeruginosa PJHU15 either singly and/or in consortia. A significant increase in total phenolic, flavonoid, ascorbic acid and protein contents, free radical scavenging activity, hydroxyl radical scavenging activity, iron chelation and reducing power were observed in the seeds and pericarp of pods treated with a consortium of microbes in comparison to control pods. Also, the differential accumulation of phenolic compounds, namely, shikimic acid, gallic acid, tannic acid, syringic acid, p-coumaric acid, quercetin and kaempferol, was observed from the HPLC chromatogram of the seed extracts of different treatments. We especially emphasized on dietary importance of the pod pericarp, other than seeds, along with their modulation by microbial consortium. The study also highlights the role of beneficial microbes in improving nutritional value by providing protection against oxidative stress. •Microbial consortium of Trichoderma harzianum, Bacillus subtilis and Pseudomonas aeruginosa was used.•Their role in modulating qualities of pea seeds and pericarp was examined.•Consortium-treated plants showed increase in total phenolic and flavonoid content.•Similar increase was seen in ascorbic acid, protein content and iron chelation.•Hydroxyl and free radical scavenging activities and reducing power also increased.