Nanocrystals of zeolites with shortened diffusional pathways compared to bulk counterparts are attractive catalysts, but their direct synthesis often remains challenging and expensive. Here, we describe the utility of p-phenylenedimethylene–bis(trimethylammonium) dichloride, an organic diquaternary ammonium compound that can be easily prepared, as an effective organic structure-directing agent (OSDA) for obtaining several zeolites composed of agglomerated nanocrystals. By modifying the gel composition (NaOH/Si and Si/Al ratios) and crystallization time, synthesis can be tuned to obtain mordenite, EU-1, and ZSM-12 zeolites. 13C NMR spectra of the occluded OSDA reveal subtle differences in host–guest interactions between the OSDA and the respective zeolites, which derives from the flexibility of the OSDA. The relatively strong interaction between the OSDA and inorganic aluminosilicate precursor species during the induction period explains how small zeolite nanocrystals are obtained. Nanosized EU-1 and ZSM-12 significantly outperform their corresponding bulk counterparts as acid catalysts in the methanol-to-hydrocarbons reaction and the alkylation of benzene with benzyl alcohol, respectively.