Geopolymer concrete is a promising alternative to traditional cement due to its lower carbon footprint and enhanced mechanical properties. While carbonatogenic bacteria have been widely studied in Portland cement, their role in geopolymers remains underexplored, particularly in non-calcium precipitation mechanisms. This study screened limestone quarry samples using 16S amplicon sequencing to identify potential carbonatogenic bacteria. Following isolation and precipitation analysis, Lysinibacillus fusiformis JH2 was selected and incorporated into fly ash-bottom ash-based geopolymer paste. XRD and SEM analysis revealed that microbial carbonation led to the formation of aragonite, natrite, and brucite, refining pore structures, enhancing durability, and increasing compressive strength. Incorporating JH2 endospores significantly improved early strength, achieving 17.5 MPa within 7 days, meeting Indonesian structural standards, and increasing strength by up to 166 %. Notably, bacteria remained viable and retained their ability to form endospores, opening possibilities for endospore storage in artificial aggregates for self-healing and bio-enhanced construction materials. These findings also show a potentially novel microbial pathway for non-calcium precipitation, contributing to the faster, more sustainable enhancement of geopolymer concrete for industrial applications.