Geopolymers offer a green alternative to cement for use in construction chemicals. This study aimed to synthesize partially cured geopolymeric structures for use in waterproofing mortars, targeting applications such as water tanks, pools, and areas exposed to seawater and rain, where preventing crack formation and water leakage is crucial. The quantity of ordinary Portland cement (OPC) in a two‐component waterproofing flexible mortar was reduced by incorporating geopolymer cured in open air under ambient conditions. Based on characterization tests, three geopolymers were selected for inclusion in the mortar formula. Fresh mortar pre‐tests and performance tests on cured mortar were conducted. The results indicated that the mortar formula containing geopolymer at 75 wt.% of OPC, with a solid/liquid weight ratio of 1.5 and a blast furnace slag/fly ash weight ratio of 75:25, where the blast furnace slag had a more amorphous structure, exhibited optimal characteristics in crack bridging, bond strength, capillary water absorption, and waterproofing capacity. This study demonstrates the effectiveness of geopolymers in reducing OPC consumption and enhancing their user‐friendliness in waterproofing mortar applications. It offers practical insights into optimizing geopolymer formulations for superior performance and environmental benefits.