Manganese-containing BEA zeolites, MnxSiBEA (x = 1–4 wt %) and Mn(I.E.)AlBEA, were prepared by a two-step postsynthesis method and a conventional wet ion-exchange, respectively, and applied as catalysts in the selective catalytic reduction of NO with ammonia (NH3-SCR). The physicochemical analysis of zeolite properties by the 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 catalysts acidity by FTIR spectroscopy with CO and pyridine probe molecules provided important insight into the number and type of acidic centres present on catalyst surface. The catalytic results revealed that NO conversion depended on the state and content of Mn. The zeolites obtained with the two-step postsynthesis method and with low Mn content were very active at medium temperature range (NO conversion ~100 %) with simultaneous high selectivity to N2 due to the presence of isolated, framework Mn(III) and Mn(II) species. The N2O formation was especially high for catalysts containing extra-framework polynuclear Mn species and negligible in the case of Mn(I.E.)AlBEA containing predominantly isolated, extra-framework Mn(II) species.