The present study was designed to synthesize the bioactive molecule 2,2-bis(2,4-dinitrophenyl)-2-(phosphonatomethylamino)acetate (), having excellent applications in the field of plant protection as a herbicide. Structure of newly synthesized molecule was confirmed by using the elemental analysis, mass spectrometric, NMR, UV-visible, and FTIR spectroscopic techniques. To obtain better structural insights of molecule, 3D molecular modeling was performed using the GAMESS programme. Microbial activities of were checked against the pathogenic strains (NCIM 902) and (NCIM 2501). Molecule has shown excellent activities against fungal strain (35 μg/l) and bacterial strain (25 μg/l). To check the medicinal significance of molecule , interactions with bovine serum albumin (BSA) protein were checked. The calculated value of binding constant of molecule-BSA complex was 1.4 × 10 M, which were similar to most effective drugs like salicylic acid. More significantly, as compared to herbicide glyphosate, molecule has exhibited excellent herbicidal activities, in pre- and post-experiments on three weeds; barnyard grass (), red spranglitop (), and yellow nuts (). Further, effects of molecule on plant growth-promoting rhizobacterial (PGPR) strains were checked. More interestingly, as compared to glyphosate, molecule has shown least adverse effects on soil PGPR strains including the (NCIM 2749), (NCIM 5096), and (NCIM 2847).