The viability of using ammonia as a hydrogen storage vector is contingent on the development of catalytic systems active for ammonia decomposition at low temperatures. Zeolite-supported metal catalysts, unlike systems based on supports like MgO or carbon nanotubes (CNTs), are crystalline and lend themselves to analytic techniques like synchrotron X-ray powder diffraction (SXRD) and Rietveld refinement, allowing precise characterisation of catalytic active sites, and therefore mechanistic elucidation. This study focuses on characterising and optimising novel zeolite-supported Ru catalysts for ammonia decomposition, with a focus on the effects of N-substitution on catalyst structure and activity. Characterisation focuses on an unsubstituted and N-substituted Ru-zeolite Y pair with NMR, FTIR, TEM, XRD, XAS, ICP, and BET, demonstrating the successful incorporation of N into the zeolite framework and an enhancement in metal dispersion upon N-substitution. A series of 18 monometallic and bimetallic catalysts is then synthesised on X and USY supports and screened for catalytic activity. Ru is identified as the most active metal for ammonia decomposition. Observed trends suggest catalyst dispersion can be increased with substantially lower metal loadings, and in particular via the formation of stably anchored oligonuclear metal clusters within the zeolite framework, as opposed to much larger nanoparticles (NPs) on its exterior, following N-substitution of the framework. DFT modelling proposes a prismatic Ru6N6 cluster fitted to XAS data. High-activity catalyst Ru-β (N) 2.4% demonstrates comparable or better ammonia conversion by Ru wt% than recently reported catalysts in the literature at 450 °C and 30 000 WHSV.