The immobilization of homogeneous catalysts onto solid supports to improve recyclability while maintaining catalytic efficiency is often a trial-and-error process limited by poor control of the local catalyst environment and few strategies to append catalysts to support materials. Here, we introduce a modular heterogenous catalysis platform that addresses these challenges. Our approach leverages the well-defined interiors of self-assembled Pd12L24 metal–organic cages/polyhedra (MOCs): through a combination of catalyst-ligands, polymeric ligands, and spacer ligands, we demonstrate facile self-assembly of novel acetylene-linked Pd12L24-crosslinked polymer gels featuring endohedrally-catalyst-functionalized junctions. Semi-empirical calculations show that catalyst incorporation into these MOC junctions does not affect their geometry, giving rise to well-defined nanoconfined catalyst domains as confirmed experimentally using electron paramagnetic resonance spectroscopy. Given the unique network topology of these freestanding gels, they are mechanically robust regardless of their endohedral catalyst composition, allowing them to be physically manipulated and transferred from one reaction to another to achieve multiple rounds of catalysis. Moreover, by decoupling the catalyst environment (interior of MOC junctions) from the physical properties of the support (the elastic polymer matrix), this strategy enables catalysis in environments where homogeneous catalyst analogs are not viable, as demonstrated for the Au(I)-catalyzed cyclization of 4-pentynoic acid in aqueous media.