Parthenium hysterophorus L. (Parthenium) is an invasive weed species which is spreading worldwide affecting natural ecological systems, biodiversity, crop production and human health. The present study was conducted to evaluate the potential of plant growth promoting Pseudomonas putida NBRIC19 in detoxifying the phytotoxic effect of Parthenium. Significant increase in C/N ratio, macronutrients, and micronutrients was observed in P. putida NBRIC19-treated soil. P. putida NBRIC19 treatment of the soil provided protection to plant communities in Parthenium invaded area, as the species diversity had increased in the treatment as compared to non-bacterized soil. P. putida NBRIC19 treatment besides Parthenium, also succeeded in controlling other weed species like Commelina benghalensis and Cynodon dactylon. In addition to this, the impact of Parthenium was also studied on functional microbial diversity based on carbon source utilization pattern. It was observed that P. putida NBRIC19 treatment of soil had shifted the microflora in such a manner that utilization of toxic allelochemicals increased to lessen their phytotoxic effect. Taken together, these results suggest that soil treatment with P. putida NBRIC19 may be used as a promising biological control measure for controlling the phytotoxic effect of Parthenium and in protecting ecosystem integrity of neighboring plants in Parthenium invaded areas.