Manganese-containing BEA zeolites, MnSiBEA (x = 1-4 wt%) and MnAlBEA, were prepared by a two-step post-synthesis method and a conventional wet ion-exchange, respectively, and applied as catalysts in the selective catalytic reduction of NO with ammonia (NH-SCR). The physicochemical analysis of zeolite properties by high-energy-resolution fluorescence-detected XANES (HERFD-XANES) and X-ray emission spectroscopy (XES) uncovered that the coordination, geometry and oxidation state of Mn species are strongly related to the preparation method. Additionally, the study of catalyst acidity by FTIR spectroscopy with CO and pyridine probe molecules provided important insight into the number and type of acidic centres present on the catalyst surface. The catalytic results revealed that NO conversion depended on the state and content of Mn. The zeolites obtained by the two-step post-synthesis method and with a low Mn content were very active in the medium temperature range (NO conversion ∼100%) with simultaneous high selectivity to N due to the presence of isolated, framework Mn(iii) and Mn(ii) species. The NO formation was especially high in the case of catalysts containing extra-framework polynuclear Mn species and negligible in the case of MnAlBEA containing predominantly isolated, extra-framework Mn(ii) species.