The microstructural development of the Zn-Mn-O system in air atmosphere is governed by the formation and thermal evolution of different Mn3-xZnxO4 spinel-type phases, whose degree of distortion varies as a function of composition and temperature. By means of X-ray powder diffractometry and X-ray absorption spectroscopy, the structure of the observed cubic C and tetragonal T1 and T2 spinels is analyzed in the present contribution. X-ray absorption near-edge structure reveals a decrease of the average Mn valence with the increasing calcination temperature. Local structures of the spinel phases have been studied using simultaneous refinement of the X-ray absorption fine structure of both metals. The analysis has found deformations of the MnO6 octahedra already in the C phase. With the orientation of these random deformations to a common c-axis, the cubic C phase transforms into the tetragonal T2 phase. With increasing temperature, the tetragonal character of the T2 phase becomes ever more pronounced as the content of Mn3+ increases and the value of x decreases. In C and T2 phases, Mn only occupies octahedral sites of the spinel structure, whereas in the T1 phase, a small degree of inversion was observed.