Current trends in the field of MXenes emphasize the importance of controlling their surface features for successful application in biotechnological areas. The ability to stabilize the surface properties of MXenes has been demonstrated here through surface charge engineering. It was thus determined how changing the surface charges of two-dimensional (2D) Ti3C2 MXene phase flakes using cationic polymeric poly-L-lysine (PLL) molecules affects the colloidal and biological properties of the resulting hybrid 2D nanomaterial. Electrostatic adsorption of PLL on the surface of delaminated 2D Ti3C2 flakes occurs efficiently, leads to changing an MXene’s negative surface charge toward a positive value, which can also be effectively managed through pH changes. Analysis of bioactive properties revealed additional antibacterial functionality of the developed 2D Ti3C2/PLL MXene flakes concerning Escherichia. coli Gram-negative bacteria cells. A reduction of two orders of magnitude of viable cells was achieved at a concentration of 200 mg L−1. The in vitro analysis also showed lowered toxicity in the concentration range up to 375 mg L−1. The presented study demonstrates a feasible approach to control surface properties of 2D Ti3C2 MXene flakes through surface charge engineering which was also verified in vitro for usage in biotechnology or nanomedicine applications.