Herein, we report the removal of organic dyes by metal–organic ionic frameworks (MOIFs) incorporating Mo7O246- and alkyl ammonium ions synthesized via an ion-exchange process in aqueous medium, [CnH2n+1)nN(CH3)3][Mo7O24], where n = 12, 14, 16. These were characterized using powder X-ray diffraction (XRD), UV/Visible spectroscopy, and Fourier-transform infrared (FTIR) spectroscopy techniques. A thermal transition occurring at 300–400 °C attributed to the decomposition of organic moieties analyzed through thermal gravimetric analysis (TGA). Coats-Redfern analysis revealed an activation energy of approximately −1.32763 kJ/mol, suggesting rapid interaction capability of MOIFs with pollutants. The heat capacity found approximately 135 J/K, indicating thermal stability investigated using differential scanning calorimetry (DSC). MOIFs exhibited remarkable adsorption of organic dyes demonstrated through complete removal (100 %) of anionic congo red dye and 88 % of cationic safranin dye. MOIFs functionalized with protein conjugates (MOIF@BSA) were evaluated for their adsorption efficiency on mix dye compared to MOIFs, displaying superior performance with up to 95 % removal of mixed dyes. Kinetic studies employing pseudo-first-order kinetics indicated that the adsorption process is primarily governed by the diffusion of dye molecules within the MOIFs structure. Desorption analysis demonstrated complete recovery of MOIFs, dyes, and solvent, highlighting the environmentally friendly nature of the approach employed, consistent with green chemistry principles.