As cement production causes large amounts of CO₂ emissions and is not sustainable, there is a growing worldwide interest in developing cleaner construction materials by reducing carbon emissions and reusing existing industrial waste. Also, antimicrobially active construction materials are gaining attention due to enhancing structural longevity. By preventing microbial growth, these materials help to improve indoor air quality and occupant health. Geopolymer mortars/concretes (GPM/GPC) with high mechanical, physical and durability properties are considered as an eco-friendly alternative to ordinary Portland cement (OPC) mortars/concretes. In this study, the composition, microstructural, mechanical and antimicrobial properties of geopolymers produced at different curing temperatures (60, 80, 100 and 120 °C) were investigated. Low-lime fly ash was used as binder and sodium silicate and sodium hydroxide were used as the alkaline solution in geopolymer production. Although X-ray fluorescence (XRF) results showed an increase in geopolymerization products with increasing temperature, SEM analysis showed that the crack formation that occurs in the microstructure of geopolymers cured above 100 °C leads to decreased mechanical properties. The strength and antimicrobial performance test results for geopolymer mortars showed that the optimum temperature was 100 °C, and the highest compressive strength (48.41 MPa) was reached at this temperature. A decrease in strength was observed due to cracks occurring in the microstructure at higher temperatures. The agar diffusion method was used to determine the antimicrobial activity of GPMs against four bacteria and one fungus species. The antimicrobial activity test results showed that the samples subjected to thermal curing at 100 °C formed the highest inhibition zones (38.94–49.24 mm). Furthermore, the alkalinity of the components/mixtures has a direct relationship with antimicrobial activity. As a result, GPMs with superior antimicrobial and mechanical properties can be considered as promising building materials, especially for construction applications where hygiene is a priority and for structures that are likely to be exposed to microbial corrosion.