The decontamination reactions of O,S-diethyl methyl phosphonothiolate, as an agricultural organo-phosphorous pesticide onto 20 wt% loaded manganese dioxide nanoparticles-silver-Y zeolite as a nanocomposite catalyst in different solvents, were evaluated and monitored by means of gas chromatography–flame ionization detector and gas chromatography–mass spectrometry. Prior to the reaction, the catalyst was synthesized in three steps: at first, sodium-Y zeolite was prepared by hydrothermal method; then, silver-Y zeolite was prepared from sodium-Y zeolite using ion exchange procedure; and finally, manganese dioxide nanoparticles were synthesized by in situ impregnation method by pouring the pre-prepared silver-Y zeolite into manganese(ΙΙ) nitrate solution and loaded as 20 wt% onto silver-Y zeolite structure. The formation of the synthesized units and final nanocomposite catalyst was verified through scanning electron microscopy, X-ray diffraction, atomic absorption spectrometry and Fourier transform-infrared spectroscopy techniques. Gas chromatography chromatograms showed that O,S-diethyl methyl phosphonothiolate was decontaminated perfectly by the catalyst in n-heptane solvent after 8 h, at room temperature, while chloroform and isopropanol solvents and other reaction times gave lower decontamination results. Moreover, gas chromatography–mass spectrometry chromatograms confirmed the formation of ethyl methyl phosphonic acid as a major and final product, which exemplifies the role of hydrolysis reaction during the degradation progress.