This study reports the use of 1-butyl-3-methyl imidazolium methanesulfonate ionic liquid as a template in the synthesis of zeolites. It is found that the silicon source determines the formation of beta (BEA), mordenite framework inverted (MFI), or analcime (ANA) zeolites. Depending on this source, different preorganized complexes are obtained that drive the formation of the different zeolite structures. In the presence of ethanol, the ionic liquid form preorganized complexes that drive the formation of MFI. In its absence, BEA is obtained. Whereas, the large amount of sodium present when using sodium metasilicate leads to ANA formation. A molecular simulation study of the relative stability of the template-framework system and location of the template provides further insight into the mechanism of synthesis.