Background: Traditionally, Carica papaya L. and Raphanus sativus L. have been used to cure a variety of illnesses. Their aqueous extracts’ antibacterial potential was to be assessed in this investigation. Methods: Materials from stems and leaves were macerated, pulverized, and shade-dried. Antimicrobial testing against E. coli using the Zone Inhibition Method (Kirby-Bauer method) with ciprofloxacin (10 μg) as positive control, FTIR analysis, and phytochemical screening were carried out. Results: phytochemical study identified proteins, carbohydrates, alkaloids, and flavonoids. There were 13 functional groups found by FTIR. At a dosage of 6.25 μg/mL, the combined extract exhibited substantial antibacterial activity with an 8 mm zone of inhibition. Conclusion: The extracts show encouraging antibacterial properties, indicating that they may be used as natural antimicrobial agents in medicinal and food preservation applications.