Biocompatible and highly fluorescent phosphorus, nitrogen and sulfur carbon quantum dots (P,N,S-CQDs) were synthesized using a quick and ecologically friendly process inspired from plant sources. Garlic and red lentils were utilized as natural and inexpensive sources for efficient synthesis of the carbon-based quantum dots using green microwave-irradiation, which provides an ultrafast route for carbonization of the organic biomass and subsequent fabrication of P,N,S-CQDs within only 3 min. The formed P,N,S-CQDs showed excellent blue fluorescence at λem= 412 nm when excited at 325 nm with a quantum yield up to 26.4%. These fluorescent dots were used as a nano-sensor for the determination of the commonly used antibacterial and antiprotozoal drug, metronidazole (MTR). As MTR lacked native fluorescence and prior published techniques had several limitations, the proposed methodology became increasingly relevant. This approach affords sensitive detection with a wide linear range of 0.5-100.0μM and LOD and LOQ values of 0.14 μM and 0.42 μM, respectively. As well as, it is cost-effective and ecologically benign. The MTT test was used to evaluate the in-vitro cytotoxicity of the fabricated P,N,S-CQDs. The findings supported a minimally cytotoxic impact and good biocompatibility, which provide a future perspective for the applicability of these CQDs in biomedical applications.