Mesoporous silica-based materials attract great interest for diverse applications, including capture, storage, and catalysis due to their large surface area, uniform pore size distribution, and customizable surface. The regular 2D hexagonal pore symmetry of MCM-41 makes it an ideal model. Amine groups are introduced to enhance CO2 adsorption, but the interplay of factors influencing overall performance, including pore size, remains unclear. This computational study explores the physisorption of CO2 and CH4, shedding light on the microscopic details underlying adsorption capacity and selectivity. Three aminopropyl-functionalized MCM-41 models with different pore size are compared through Grand Canonical Monte Carlo and Molecular Dynamics simulations. Aminopropyl chains affect CO2 adsorption, but its affinity for the preserved silanol groups is larger. In addition, the competitive interaction between amine and silanol groups emerged, and it is pore curvature dependent. Surprisingly, CH4 physisorption is influenced even more by surface functionalization. Results show a non-monotonic trend as a function of pore size. Local density of the alkyl chains plays the major role. Overall, the intermediate pore size demonstrates the best performance, thanks to the balance among the various effects. The study emphasizes the importance of understanding the interplay between material texture and gas interactions to optimize adsorption performance.