Bacterial infections are of major medical concern due to antibiotic resistance. Carbon quantum dots (CDs) have emerged as potentially excellent biomaterials for multifunctional applications due to their low toxicity, outstanding water solubility, high fluorescence, and high biocompatibility. All of these properties allow CDs to be exceptional biomaterials for inhibiting the growth of bacteria and stopping biofilm formation due to their strong binding affinity, cell wall penetration, and solubilizing biofilm in water. Here, we describe a strategy for one-pot synthesis of histidine-derived zinc-doped N-doped CDs (Zn-NCDs) by a hydrothermal method for inhibiting the growth of both Gram-positive and Gram-negative bacteria without harming mammalian cells. The NCDs and Zn-NCDs showed uniform sizes (∼6 nm), crystallinity, good photostability, high quantum yield (76%), and long decay time (∼5 ns). We also studied their utilization for live cell bio-imaging and the antimicrobial properties towards the Gram-positive Staphylococcus aureus and the Gram-negative Pseudomonas aeruginosa. Importantly, the Zn-NCDs could penetrate the biofilm and bacterial cell wall to effectively inhibit the growth of bacteria and subsequently inhibit biofilm formation. Thus, the structure, chemical composition, and low toxicity properties of the newly-developed Zn-NCDs exemplify a promising novel method for the preparation of nano-level antibacterial drugs.