In the present study, Carbon Quantum Dots (CQDs) were synthesized from Phoenix dactylifera (Date palm fruit) using microwave-assisted pyrolysis and were characterized for its various properties. The synthesized CQD sample exhibited a narrow absorbance peak at 270 nm in UV–Vis spectrum that indicated generation of narrow sized particles. The FTIR analysis of the crude CQDs and dialysed sample revealed the various functional groups involved in the formation of CQDs. TEM data revealed the nature of CQDs to be quasi-spherical and spatially distributed. Biocompatibility of the CQDs was studied using various model systems. CQDs displayed no cytotoxic and anti-clonogenic property when exposed to WRL-68 cell line whereas a slight toxicity was evident in HT1080 post 24 h of incubation suggesting the tremendous potential of the CQDs in the synergistic killing of cancer cells. Phytotoxicity assessment in four different seedlings revealed the non-toxic nature of CQDs. Further these CQDs were found to possess high biocompatibility imposing no inhibition in microbial growth and zilch effect on the development of zebrafish embryos. Thus these CQDs can find immense potential applications in fields of biomedicine as biomolecule detection, drug carriers, fluorescent tracers and in controlling the drug release.