A series of organic-inorganic composite catalysts, prepared by modifying tungstophosphoric acid (TPA; H3PW12O40) with different amino acids such as phenylalanine (Phe), alanine (Ala), and glycine (Gly) were synthesized. The physicochemical and acidic properties of these (MH)xH3−xPW12O40 (M=Phe, Ala, and Gly; x=1–3) composite materials were characterized by a variety of different analytical and spectroscopic techniques, namely TGA, XRD, FT-IR, XPS, and NMR, and exploited as heterogeneous catalysts for selective oxidation of benzyl alcohol (BzOH) with hydrogen peroxide (H2O2). Among them, the [PheH]H2PW12O40 catalyst exhibited the best oxidative activity with an excellent BzOH conversion of 99.0% and a desirable benzaldehyde (BzH) selectivity of 99.6%. Further kinetic studies and model analysis by response surface methodology (RSM) revealed that the oxidation of BzOH with H2O2 follows a second-order reaction with an activation energy of 56.7 kJ·mol−1 under optimized experimental variables: BzOH/H2O2 molar ratio=1 : 1.5 mol/mol, amount of catalyst=6.1 wt%, reaction time (x3)=3.8 h, and amount of water (x4)=30.2 mL.