Selective catalytic reduction with ammonia (NH3-SCR) is a widely used deNOx process, employing zeolitic catalysts. Here, we examine framework substituted and extra-framework exchanged transition metal zeolite catalysts, in the extensively studied Fe – zeolite Beta focusing on the influence of the transition metal cation on the NH3-SCR reaction, and aiming to unravel the underlying mechanisms and their impact on catalytic performance. We use hybrid multiscale density functional theory (DFT)/molecular mechanics to investigate the NH3-SCR at various Fe-BEA active sites including systems with both framework and extra-framework Fe cations. The catalytically active sites under investigation include Fe-FeF-BEA, Fe-AlF-BEA, and Cu-FeF-BEA, (where the subscript F indicates framework species) on which the formation and consumption of key intermediates of both oxidation and reduction half cycles species are analysed. We show the distinctive ability of framework Fe sites to promote the formation of key nitrate and nitrosamine intermediates. Furthermore, we find a strong binding affinity of NH3 with framework Fe systems including Cu(II)-FeF-BEA, Fe(III)-FeF-BEA, and H-FeF-BEA compared to framework Al systems (Fe(III)-AlF-BEA). We explore the reduction potential of the framework Fe3+/Fe2+ in BEA zeolite and establish its feasibility in the presence of a Brønsted acid site. Our calculations clearly predict the bimetallic Cu-FeF system to be the best catalyst which supports a recent experimental report by Yue et al. (Chem. Eng. J. 2020, 398, 125515) for a related FeCu-SSZ-13 (CHA) zeolite. We provide a new understanding of the reactivity of Fe-BEA zeolites, suggesting the advantages of framework Fe over Al sites in NH3-SCR reactions, and establishing a foundation for interpretation of the rôle of framework cations in metal-exchanged zeolites.