Fluid-rock interactions may differ in mesopores (2–50 nm diameter) compared to macropores (>50 nm diameter). This study evaluates the influence of nano-confinement and pore geometry on point of zero charge (PZC) and hence surface charge and adsorption. PZC was determined for a suite of synthetic mesoporous amorphous silica materials and compared to the PZC of macroporous and non-porous amorphous silica. Reactive molecular dynamics simulations using ReaxFF determined surface equilibrium constants (pK) and clarified the large range of PZC values reported for macroporous and non-porous amorphous silica. Potentiometric titrations measured PZC and pK values of three mesoporous amorphous silica materials (SBA-15, SBA-16, and MCM-41) possessing a range of pore diameters (∼4–13 nm) and distinct pore geometries (cylindrical pores in a hexagonal lattice, spherical pores in a body-centered-cubic lattice, and hexagonal pores arranged in a hexagonal lattice); fluids were pre-saturated with silica to inhibit reaction with pore walls. Results are integrated with data from more than 150 published experimental studies. Neither nano-confinement nor pore geometry affects the PZC of the mesoporous amorphous silica materials. These results have implications for adsorption chemistry under confinement in mesoporous siliceous natural systems such as shales.