In this study, nickel-doped aminosilica membranes containing pendant groups were prepared with 3-aminopropyltriethoxysilane (APTES), trimethoxy[3-(methylamino)propyl]silane (MAPTS), 3 N,N-dimethyl aminopropyltrimethoxysilane (DAPTMS), N-[3-(trimethoxysilylpropyl]ethylene diamine (TMSPED), and 1-[3-(trimethoxysilyl)propyl] urea (TMSPU). Differences in the structures of terminal amine ligands significantly contributed to the formation of a coordinated structural assembly. Ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), and N2 adsorption isotherms revealed that short and rigid pendant amino groups successfully coordinated with nickel to produce subnanopores in the membranes, while an ion-exchange interaction was suggested for longer and sterically hindered aminosilica precursors. Moreover, the basicity of amine precursors affected the affinity of ligands for the development of a coordinated network. A pristine aminosilica membrane showed low levels of H2 permeance that range from 0.1 to 0.5 × 10-6 mol m-2 s-1 Pa-1 with a H2/N2 permeance ratio that ranges from 15 to 100. On the contrary, nickel coordination increased the H2 permeance to 0.1-3.0 × 10-6 mol m-2 s-1 Pa-1 with H2/N2 permeance ratios that range from 10 to 68, which indicates the formation of a microporous structure and enlargement of pore sizes. The strong level of coordination affinity between nickel ions and amine groups induced rearrangement of the flexible pendant chain into a more rigid structure.