Microporous hybrid silica membranes are known to have superior (hydro)thermal and chemical stability. By incorporating metal ions, such as Ce4+ and Ni2+ into these membranes, their affinity and selectivity towards particular gases may be altered. To promote the dispersion of metal ions within the hybrid silica matrix, the sol–gel precursor N,N,N′,N′-tetrakis-(3-(triethoxysilyl)-propyl)-malonamide (TTPMA) was synthesized. The malonamide ligands clearly coordinated the Ce4+ and Ni2+ metal centers and enhanced their dispersion. During annealing these metal centers redistributed into small nanosized grains of CeO2 (<5 nm) and Ni2O3 (<15 nm). These Ce-TTPMA and Ni-TTPMA membranes showed higher H2/N2 permselectivities as compared to previously reported hybrid silica membranes based on the 1,2-bis-(triethoxysilyl)ethane precursor. The TTPMA-precursor was found suitable for membrane separation and can be a promising and versatile precursor for the incorporation of metal ions within hybrid silica matrices.