A variety of zeolites have been synthesized by performing either metakaolinization or fused-metakaolinization of natural clays prior to the hydrothermal synthesis step. To understand the differences arising from performing fused metakaolinization rather than simple metakaolinization, the calcination conditions, gel composition, gelling and crystallization conditions were kept similar for both methods. The original clay material, a kaolinite group mineral with Si/Al molar ratio of 1, had a high content of quartz as impurity. The two treatment methods gave different zeolites of high crystallinity and relatively similar Si/Al molar ratio. Zeolite Na-A with 98% crystallinity was produced from the metakaolinization method within 8 h, while Na-X with 96% crystallinity was generated from the fused-metakaolinization (fusion) method within 48 h. In the fusion method, sodalite was formed at or beyond 48 h of hydrothermal reaction, while in the metakaolinite method, apart from a slight decrease in intensities of XRD peaks, no phase change was observed even after 168 h of hydrothermal reaction. Modification of the synthesis gel by increasing the Si/Al molar ratio via addition of fumed silica resulted in mixed zeolite products via the metakaolinite method, while Na–Y was the major product for the fusion method. Except for Na-A, all zeolite products had high surface area of up to 600 m2/g and micropore volume of 0.18 cm3/g. Our findings demonstrate the crucial role of the pre-treatment step in the synthesis of zeolites from clay minerals, and that a variety of high quality zeolites are achievable via choice of pre-treatment protocols.