Effective encapsulation strategies are highly sought-after in heterogeneous catalysis for preparing highly active and stable metal (oxide) nanocatalysts. Herein, we report an optimized Melt Infiltration (MI) procedure to confine nickel(oxide) nanoparticles (NPs) into hierarchical microporous-mesoporous scaffolds. Three SBA-15 silicas were synthesized in order to obtain different degrees of interconnectivity between the main mesopores. The impact of the SBA-15 pore characteristics, i.e., this interconnectivity, also named secondary intra-wall porosity (IWP), on the final nickel (oxide) NPs size and localization has been specifically investigated. Using MI, which consisted in the diffusion of the precursor in the liquid state inside the porosity of the support in the presence of the native surfactant occluding the pores, a selective localization of the NiO NPs inside the IWP was obtained, without large NPs plugging the main mesopores if IWP pores connecting the main mesopores do exist. When IWP – selective localization – occurs for the NPs, they show a size directly depending on the IWP dimensions. The obtained materials were tested, after reduction, in the hydrogenation reactions of cinnamaldehyde and 5-hydroxymethylfurfural. The catalytic results underline the positive effect of IWP – confinement of NPs to obtain and maintain an elevated dispersion of the metallic Ni active phase and to reach a high catalytic activity in hydrogenation under mild reaction conditions.