Two-dimensional (2D) MXenes have demonstrated outstanding antimicrobial properties owing to their unique physiochemical properties and ultrathin lamellar structure. However, the relationship between MXene sheet size and its antimicrobial activity and how the atomic structure can impact the antibacterial mechanism are yet to be revealed. This study investigates the effect of atomic structure and size dependency on the antibacterial activity of two niobium carbide MXenes (Nb2CTx and Nb4C3Tx) using model Gram-negative and Gram-positive bacteria. The results showed that the bactericidal property of Nb2CTx and Nb4C3Tx against Escherichia coli and Staphylococcus aureus is dependent on the sheet size and atomic structure of both MXenes. 120 $\mu$g/mL delaminated (DL)-Nb2CTx and DL-Nb4C3Tx exhibited growth inhibition of 94.2 and 96.1% for E. coli and 91.6 and 93.7% for S. aureus cells within 3 h of incubation, respectively. The bacterial cell viability decreased with decreasing lateral sheet size of DL-Nb2CTx and DL-Nb4C3Tx down to 160 and 183 nm, respectively. DL-Nb4C3Tx-183 showed higher antibacterial activity than DL-Nb2CTx-160 because of a higher c lattice parameter. Moreover, DL-Nb4C3Tx-183 demonstrated higher oxidative stress on both bacterial cells in comparison with DL-Nb2CTx-160. This study highlights the role of the atomic structure of MXenes and the importance of tailoring the lateral size of the nanosheets to optimize the bactericidal properties of 2D nanomaterials.