The widespread of bacterial infections including biofilms drives the never-ending quest for new antimicrobial agents. Among the great variety of nanomaterials, carbon dots (CDs) are the most promising antibacterial material, but still require the adjustment of their surface properties for enhanced activity. In this contribution, we report a facile functionalization method of carbon dots (CDs) by tetraalkylammonium moieties using diazonium chemistry to improve their antibacterial activity against Gram-positive and Gram-negative bacteria. CDs were modified by novel diazonium salts bearing tetraalkylammonium moieties (TAA) with different alkyl chains (C2, C4, C9, C12) for the optimization of antibacterial activity. Variation of the alkyl chain allows to reach the significant antibacterial effect for CDs-C9 towards Gram-positive Staphylococcus aureus (S. aureus) (MIC = 3.09 ± 1.10 μg mL−1) and Gram-negative Escherichia coli (E. coli) (MIC = 7.93 ± 0.17 μg mL−1) bacteria. The antibacterial mechanism of CDs-C9 is ascribed to the balance between the positive charge and hydrophobicity of the alkyl chains. TAA moieties are responsible for enhanced adherence on the bacterial cell membrane, its penetration and disturbance of physiological metabolism. CDs-C9 were not effective in the generation of reactive oxygen species excluding the oxidative damage mechanism. In addition, CDs-C9 effectively promoted the antibiofilm treatment of S. aureus and E. coli biofilms outperforming previously-reported CDs in terms of treatment duration and minimal inhibitory concentration. The good biocompatibility of CDs-C9 was demonstrated on mouse fibroblast (NIH/3T3), HeLa and U-87 MG cell lines for concentrations up to 256 μg mL−1. Collectively, our work highlights the correlation between the surface chemistry of CDs and their antimicrobial performance.