The addition of heteroatoms to pristine carbon quantum dots (CQDs) change their structure and optical properties. In this study, fluorine (F)- and chlorine (Cl)-doped CQDs are prepared by the one-step green hydrothermal route from sodium fluoride, sodium chloride, urea, and citric acid as the starting precursors. Microscopy analysis reveals that the average size of these quantum dots is 5 ± 2 nm, whereas the chemical study shows the existence of C–F and C–Cl bonds. The produced F- and Cl-doped CQDs have fluorescence quantum yields of 0.151 and 0.284, respectively, at an excitation wavelength of 450 nm. Charge transfer resistance of F- and Cl-doped CQDs films is 2 orders of magnitude higher than in the pristine CQD films. Transport band gap of the doped CQDs is 2 eV bigger than that of pristine CQDs. Radical scavenging activity shows very good antioxidant activity of doped CQDs. Antibacterial testing reveals poor antibacterial activity against Staphylococcus aureus and Escherichia coli. The F- and Cl-doped CQDs are successfully used as fluorescent probes for cell imaging as shown by confocal microscopy.