We report on the synthesis and characterization of spinel In-Ga-Zn-O (IGZO) thin films, having application as channel of thin-film transistors (TFTs). To obtain the spinel IGZO phase, the deposition of the IGZO was carried out on a spinel Ga-Zn-O (GZO) layer, followed by annealing in forming gas (i.e., a gas mixture of 10% H2 and 90% N2). We investigated the structural and crystallographic properties of the IGZO. To do this, we employed X-ray Diffraction and Transmission Electron Microscopy, in particular Precession Electron Diffraction. During this study, we observed the segregation of In and In2O3 phases in the IGZO. Therefore, we were interested in understanding: (i) the location of the segregated phases, (ii) the crystal orientation of IGZO, GZO, In and In2O3 phases, (iii) the impact of GZO thickness, and (iv) the temperature effect during the forming gas annealing. We found that In and In2O3 phases form nanoparticles at the surface of the IGZO. At high annealing temperature (above 420 °C), small In and In2O3 grains form also in the IGZO matrix. We explain that this is due to the reduction effect which the H in the forming gas annealing induces on the In-O species present in the IGZO crystal. Other crystallographic characteristics, such as the texture of the IGZO and the grain sizes, are related to the properties of the GZO template. In summary, this work evidenced the phase segregation in the IGZO and its crystallographic properties, both paramount for the performances of the IGZO TFTs.