The thermal decomposition of manganese borohydride Mn(BH4)2 was studied by means of synchrotron-based X-ray absorption spectroscopy (XAS), X-ray powder diffraction (XRPD) and theoretical density functional (DFT) modeling aiming to elucidate changes of the local atomic structure upon hydrogen desorption and to determine possible decomposition reaction products. XRPD patterns indicate profound structural changes in the material above 120 °C with subsequent amorphization. DFT simulations predict the collapse of the highly porous framework structure upon hydrogen desorption and significant reduction of Mn-B and Mn-Mn interatomic distances by 19% and 41% respectively. These estimations are in a good agreement with the quantitative analysis of the X-ray absorption spectra above Mn K-edge. Based on XAS we derive possible decomposition products and reaction path. In particular, the amount of Mn metallic phase was estimated to be less than 5% after the heating up to 200 °C. Several structural models for the final state of manganese borohydride in a heating process are constructed by means of energy minimization in conjunction with evolutionary algorithms.