Anode materials with high specific capacity, long service life, short charging times, high energy density and low cost should be used to meet the current requirements for lithium-ion batteries. By fine-tuning the low cost and environmentally friendly transition metal oxides, which react through a conversion mechanism with lithium, higher energy density lithium ion devices could be achieved. Despite the promising properties shown by the conversion electrodes, their commercial application is dented by factors such as rather complex phase transitions, voltage hysteresis which affects the efficiency, additional capacity resulting from electrolyte decomposition and interfacial storage and poor cycling stability of pristine materials due to contact loss and reduced electrical conductivity. Therefore, to fully understand all these parameters, even deeper knowledge of the conversion reaction pathways than currently available is still required. In the current study, spinel type mixed-transition metal ferrites, MFe2O4 (M = Fe, Co, Ni, Cu and Zn) were investigated as conversion type model systems for LIB anodes to elucidate the influence of partial substitution of Fe in the structure, Fe3O4, with different 3d-cations. The phase formation and microstructure development during the first charge-discharge process were investigated using combined in situ synchrotron powder diffraction and X-ray absorption spectroscopy techniques. During the irreversible initial discharge, a two phase mechanism is observed. Both main phase and lithiated phase crystallize in Fd-3m space group, however, in the lithiated phase the atoms occupying 8a tetrahedral sites are displaced to 16c octahedral sites together with the intercalation of lithium into 16c and 8a sites. With further lithiation crystalline material transforms to an amorphous and inhomogeneous product consisting of metallic nanoparticles in a Li2O matrix. During the following charge process metal nanoparticles are converted to binary oxides different from the parent material.