Phyllanthus niruri is a traditional herb of profound ethno-medicinal importance due to its broad-spectrum prophylactic and therapeutic attributes. All the plant parts are used for medicinal purposes. Dried powder of this medicinal plant is susceptible to microbial spoilage during post harvest processing and storage thus affecting its microbiological safety, shelf life and marketability. Therefore the current study was aimed to explore the possibility of employing gamma radiation treatment for microbial hygienization followed by comprehensive assessment of the functional bioactivities including antioxidant capacity and antimutagenic potential. The total aerobic plate count varied in the range of 3–5 log cfu/g which reduced to below detection limit upon gamma radiation treatment at a dose of 10 kGy. Besides helping in achieving hygienization, gamma radiation worked for value addition through prominent increase in the total soluble phenolics content for root, stem and leaf to 2.8, 2.2 and 1.6 times, respectively. Accordingly, significant variation was too noticed among the functional attributes (antioxidant capacity and antimutagenic potential) of different plant parts. Radiation treatment enhanced the antimutagenic potential of the leaf fraction from 52% to 74% upon radiation treatment. Current findings thus provide credible scientific evidence ascertaining the dual functional role of radiation treatment in context of herbal preparation.