Microbialites are organosedimentary rocks that have occurred throughout the Earth's history. The relationships between diverse microbial metabolic activities and isotopic signatures in biominerals forming within these microbialites are key to understanding modern biogeochemical cycles, but also for accurate interpretation of the geologic record. Here, we performed detailed mineralogical investigations coupled with NanoSIMS (Nanoscale Secondary Ion Mass Spectrometry) analyses of pyrite S isotopes in mineralising microbial mats from two different environments, a hypersaline lagoon (Cayo Coco, Cuba) and a volcanic alkaline crater lake (Atexcac, Mexico). Both microbialite samples contain two distinct pyrite morphologies: framboids and euhedral micropyrites, which display distinct ranges of delta S-34 values(1). Considering the sulfate-sulfur isotopic compositions associated with both environments, micropyrites display a remarkably narrow range of Delta(pyr) (i.e. Delta(pyr) equivalent to delta S-34(SO4) - delta S-34(pyr)) between 56 and 62 parts per thousand. These measured Delta(pyr) values agree with sulfate-sulfide equilibrium fractionation, as observed in natural settings characterised by low microbial sulfate reduction respiration rates. Moreover, the distribution of S isotope compositions recorded in the studied micropyrites suggests that sulfide oxidation also occurred at the microbialite scale. These results highlight the potential of micropyrites to capture signatures of microbial sulfur cycling and show that S isotope composition in pyrites record primarily the local micro-environments induced by the microbialite.