A combination of postsynthesis modifications and ion exchange aiming to obtain basic cation-rich hierarchical zeolites X and Y was utilized in this work for the preparation of catalysts for biofuel production from vegetable oils. The secondary mesopore system with a narrow pore size distribution in the 4 nm range was introduced by successive acid and base treatments accompanied by surfactant templating. This was followed by ion exchange with Cs+ and K+ cations to produce strong basic catalysts. The prepared hierarchical zeolites were characterized by X-ray diffraction, scanning electron microscopy, nitrogen adsorption, Fourier transform infrared spectroscopy, and solid-state NMR. The transesterification reaction over the zeolite catalysts was performed in a microwave batch-type reactor, and the effects of the reaction conditions, basic properties, and pore structure of the hierarchical faujasites were studied in detail. The conversion of triglycerides increased with increasing concentration of Cs and K in modified zeolites but declined with decreasing framework aluminum content. The balance between the strength of the basic sites and their accessibility in hierarchical zeolites and its effect on the catalytic performance of these nanostructured materials is discussed.