The present study was carried out to evaluate the influence of biofertilizers on biomass, phytochemical constituents and free radical scavenging activity of Ruta graveolens and Vitex trifolia. The plants are treated with different biofertilizers (Rhizobium leguminosarum, Azotobacter chroococum, Glomus intraradices, vermicompost) and NPK for three months. The preliminary phytochemical analysis was carried out using standard methods. Total phenolic content and DPPH scavenging activity were analysed in different plant parts. Maximum biomass was observed in G. intraradices treated plants. Phytochemical screening revealed the presence of flavonoids, proteins and amino acids, steroids, saponins, terpenoids and coumarins in the aqueous extract of root, stem and leaf of both the plants. The phenolic content was higher in A. chroococum treated R. graveolens and G.intraradices treated V. trifolia. The free radical scavenging activity was higher in G. intraradices treated plants. Our study suggests that biofertilizers treated plants enhanced the biomass, accumulation of secondary metabolites and antioxidant activity.