This study aimed to evaluate the impact of a two-step modification process involving kaolinite and cloisite Na+ on the storage stability of rubberized binders. The process involved the manual combination of virgin binder PG 64-22 with crumb rubber modifier (CRM), which was heated to condition it. The preconditioned rubberized binder was then modified for two hours at a high speed of 8000 rpm using wet mixing. The second stage modification was performed in two parts, with part 1 using only crumb rubber as the modifier and part 2 involving the use of kaolinite and montmorillonite nano clays at a replacement percentage of 3% to the original weight of the binder along with the crumb rubber modifier. The Superpave and multiple shear creep recovery (MSCR) test methods were used to calculate the performance characteristics and separation index % of each modified binder. The results showed that the viscosity properties of kaolinite and montmorillonite improved the performance class of the binder, with montmorillonite demonstrating greater viscosity values than kaolinite even at high temperatures. Additionally, kaolinite with rubberized binders showed higher resistance to rutting, and the % recovery value from multiple shear creep recovery testing indicated that kaolinite with rubberized binders was more effective than montmorillonite with rubberized binders, even at higher load cycles. The use of kaolinite and montmorillonite reduced phase separation between the asphaltene phase and rubber-rich phase at higher temperatures, but the performance of the rubber binder was affected by higher temperatures. Overall, kaolinite with the rubber binder generally demonstrated greater binder performance.