The diffusion potentials can cause significant errors in corrosion-related investigations of reinforced concrete structures (half-cell potential mapping, potentiometric sensors). Therefore, an improved understanding of the diffusion potentials in cement-based materials is needed. This study investigates the permselective behavior and its implication for the arising diffusion potentials. A diffusion cell is used to study the diffusion potentials in hardened cement pastes with imposed NaCl gradients. The cement pastes consist of ordinary Portland cement (OPC) and blast furnace cement (BFC) with water-cement ratios of 0.30–0.70. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is used to determine the concentration profiles of Cl, Na, K and Ca in the cement pastes with a high spatial resolution (100 µm). For the BFC pastes, considerable differences in the Cl−and Na+mobilities are found, indicating their permselective behavior. Despite the permselective behavior, the measured diffusion potentials are small (− 6 to + 3 mV) for all investigated cement pastes due to the high pH levels (13–14) in the pore solutions. However, when using the diffusion cell, the pH differences interfere with the measured diffusion potentials. The interfering pH differences need to be considered for an accurate measurement of the diffusion potentials in cement pastes.