Molybdenum (Mo) tends to form highly mobile, non-sorbing complex redox species, which complicates its immobilization and encapsulation in cement and glass matrices. This study explores the potential of incorporating Mo into an alternative green cementitious material known as geopolymer (GP). By employing X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), morphological analysis, and nitrogen adsorption-desorption techniques, we obtained comprehensive insights into the chemical behavior of Mo and its impact on the morphology and structure of the GP matrix. XRD and TGA analysis demonstrated that increasing Mo content significantly enhances the crystallinity and thermal stability of the GP matrix, attributed to Mo field effects. High-resolution SEM, TEM, and EDS mapping revealed the structural encapsulation of Mo-rich cavities within the GP waste form. A decrease in leaching rates with higher Mo content, alongside reduced pore volume and pore size, underscores the material's chemical durability. Post-leaching characterizations confirmed that the GP retains excellent structural strength with minimal changes in mesoporosity and surface area. This resilience highlights the effectiveness of GPs in immobilizing non-sorbing species like MoO32−, making them ideal for long-term waste management.