In the current investigation, we have reported on the preparation of mordenite zeolite nanostructures using a low-cost hydrothermal treatment of silica gel, aluminum nitrate, and sodium hydroxide. The influence of organic templates such as ethylene glycol, glycerol, and polyethylene glycol 200 (PEG 200) on the zeolite products was studied. The crystallite sizes of the as-fabricated samples increased in the following order: (PEG 200) < (ethylene glycol) < (glycerol) < (without template). The PEG 200 organic template generated a mordenite product with 57.51 nm crystallite size and 28.26 m2/g BET surface area. The as-prepared products were identified using FE-SEM, FT-IR, XRD, HR-TEM, and BET analysis. The as-prepared mordenite product could be successfully applied to purify the crude soybean oil from the yellow and red colors. The mordenite product also showed good adsorption properties toward the removal of methylene blue (MB) dye from wastewater. Kinetic data exhibited that the dye adsorption process obeyed pseudo-first-order, intra-particle diffusion, liquid film diffusion, and pore diffusion models whereas the rate determining step of the adsorption is only controlled by the pore diffusion model. Adsorption data fitted well both Langmuir and Dubinin–Radushkevich (D–R) isotherm models. Moreover, the adsorption is a physisorption and exothermic process.