The synthesis and characterization of spinel cobalt-based metal oxides (MCo2O4) with varying 3d-transition metal ions (Ni, Fe, Cu, and Zn) were explored using a hydrothermal process (140 °C for two hours) to be used as alternative counter electrodes for Pt-free dye-sensitized solar cells (DSSCs). Scanning electron microscopy (SEM) and atomic force microscopy (AFM) revealed distinct morphologies for each metal oxide, such as NiCo2O4 nanosheets, Cu Co2O4 nanoleaves, Fe Co2O4 diamond-like, and Zn Co2O4 hexagonal-like structures. The X-ray diffraction analysis confirmed the cubic spinel structure for the prepared MCo2O4 films. The functional groups of MCo2O4 materials were recognized in metal oxides throughout Fourier transform infrared (FTIR) analysis. The local structure analysis using X-ray absorption fine structure (XAFS) at Fe and Co K-edge identified octahedral (Oh) Co3+ and tetrahedral (Td) Co2+ coordination, with Zn2+ and Cu2+ favoring Td sites, while Ni3+ and Fe3+ preferred Oh active sites. Further investigations utilizing the Fourier transformation (FT) analysis showed comparable coordination numbers and interatomic distances ranked as Co-Cu > Co-Fe > Zn-Co > Co-Ni. Furthermore, the utilization of MCo2O4 thin films as counter electrodes in DSSC fabrication showed promising results. Notably, solar cells based on CuCo2O4 and ZnCo2O4 counter electrodes showed 1.9% and 1.13% power conversion efficiency, respectively. These findings indicate the potential of employing these binary metal oxides for efficient and cost-effective photovoltaic device production.