This work aims at learning how the size of gold nanocarriers influences the transport of DNA-alkylating antitumoral drugs. For this purpose, we devised conjugates of mercaptoethylmitomycin C (MEMC), a DNA alkylating agent, with gold nanoparticles of different sizes (2, 5, and 14 nm), and studied how size affects drug cytotoxicity, tumor penetrability, cellular uptake, and intracellular localization using two-dimensional (2D) and three-dimensional (3D) cell models. We show that only small, 2 nm, nanoparticles can transport MEMC efficiently to the cell nucleus, whereas MEMC cell uptake is much lower when delivered by these small nanoparticles than with the larger ones. 3D cellular models showed that smaller nanoparticles can transport MEMC toward deeper areas of tumor spheroids as compared to larger nanoparticles. We discuss the insights of this work toward the efficient delivery of DNA-targeting drugs.