Silica sinter is a subaerial hot-spring deposit formed upon cooling (<100 °C) of discharging alkali-chloride waters. Silica deposition traps and fossilizes living microbes in low-temperature (<35 °C) to mid-temperature (∼ 35–59 °C) apron–terrace outflow channels and pools, which record distinctive macrotextures and microtextures along a thermal gradient. Sinters from four geothermal fields, Orakei Korako, northern Waiotapu, Te Kopia, and Umukuri, within the Taupo Volcanic Zone, New Zealand, were sampled from two common microbe-rich microfacies (low-temperature palisade, mid-temperature bubble mat) through a range of ages (modern to ∼40 000 years BP). We observed morphologic changes in microbial silicification and stepwise transitions in silica phase mineralogy throughout diagenesis (opal-A to quartz). X-ray powder diffractometry analysis of Taupo Volcanic Zone sinter samples revealed that mode of microbial fossilization is controlled by silica phase mineralogy, which also determines the preservation potential of environmentally significant and measurable filament parameters. Typical low-temperature palisade microfacies display thick sheaths (>3 μm diameter) and coarse tubular filament moulds >5 μm in diameter, whereas mid-temperature bubble mat microfacies characteristically consist of thin sheaths (∼ 1 μm diameter) with fine moulds < 3 μm in diameter. Upon diagenesis and silica phase transformation to opal-CT, the two subenvironments cannot be distinguished based on filament diameter alone. This study of recurring microfacies in sinters of different ages allowed us to systematically track the transformation of mineralogical and morphological changes in biotic–abiotic depositional elements during diagenesis of silica sinter, and therefore enhance the paleoenvironmental, paleobiological, and paleohydrologic utility of hydrothermal deposits in the geologic record.