The study design correlates the potential of microbial strains isolated from okra and eggplant phyllosphere to degrade the commonly used organo-pesticides, chlorpyrifos (CP) and cypermethrin (CY). Phyllosphere microbes are the first to interact with sprayed pesticides and initiate key metabolic processes that may be involved in biodegradation, helping identify important intermediates and possible degradation pathways. Six isolates belonging to Bacillus sp., Pseudomonas sp., and Azotobacter sp. were tested for pesticide degradation in a mineral salt medium supplemented with 50 ppm of the individual pesticides. Samples were collected at different time intervals for Gas Chromatography-Mass Spectrometry (GC-MS/MS) analysis of the pesticide residues. The statistical significance of the degradation was assessed using one-way analysis of variance (ANOVA) (p <0.05). All six isolated bacterial strains exhibited varying degrees of pesticide degradation. The maximum degradation was recorded for CP (up to 85%) and for CY (up to 68%) by strain Azotobacter chroococcum (76A). The ANOVA results confirmed statistically significant differences in degradation rates among the strains (p <0.05), indicating diverse biodegradation efficiencies. The main identified metabolites were 3,5,6-trichloro-2-pyridinol (TCP) from CP and 3-Phenoxybenzaldehyde (3-PBA) from CY. Both secondary metabolites exhibited lower acute toxicity than their parent compounds. These findings suggest that Azotobacter strain 76A could be used as a valuable tool in bioremediation strategies. The results of this study align with previous reports that highlight the dual role of Azotobacter in nitrogen fixation and xenobiotic degradation. Overall, integrating microbiological expertise with advanced chemical analyses supports sustainable innovations and promotes safer agricultural practices.