Abstract Properties and characteristics of fly ash- or slag-based geopolymers have been extensively explored but comparatively less information is available for natural pozzolan-based geopolymers. The present work focuses on microstructural characteristics of natural pozzolan-based geopolymers activated by sodium hydroxide and a mixture of sodium hydroxide and sodium silicate. Synchrotron XRD and SEM-EDS studies combined with compressive strength tests successfully demonstrate the feasibility of the use of natural pozzolan for sustainable construction material. It is concluded that the geopolymers have sufficient strength as structural materials and matrices contain C–S–H like crystal as well as zeolites of hydroxysodalite and zeolite Y. Two zeolites of hydroxysodalite and zeolite Y are found as the main activation products in sodium hydroxide activation. Substitution with sodium silicate solution yields higher compressive strength and a denser microstructure with dominant activation products of C–S–H like crystal, zeolite Y, and phillipsite. It has been proposed that the crystal size of the activation products ranges from 10 nm to 1 μm. Different microstructural characteristics found herein provide a valuable information to develop natural pozzolan-based sustainable structural materials with improved properties.