Iron and sulfur isotope compositions recorded in ancient rocks and minerals such as pyrite (FeS2) have been widely used as a proxy for early microbial metabolisms and redox evolution of the oceans. However, most previous studies focused on only one of these isotopic systems. Herein, we illustrate the importance of in-situ and coupled study of Fe and S isotopes on two pyrite nodules in a c. 2.7 Ga shale from the Bubi Greenstone Belt (Zimbabwe). Fe and S isotope compositions were measured both by bulk-sample mass spectrometry techniques and by ion microprobe in-situ methods (Secondary Ion Mass Spectrometry, SIMS). Spatially-resolved analysis across the nodules shows a large range of variations at micrometer-scale for both Fe and S isotope compositions, with δ56Feδ56Fe and δ34Sδ34S values from −2.1 to +0.7‰+0.7‰ and from −0.5 to +8.2‰+8.2‰, respectively, and Δ33SΔ33S values from −1.6 to +2.9‰+2.9‰. The Fe and S isotope variations in these nodules cannot be explained by tandem operation of Dissimilatory Iron Reduction (DIR) and Bacterial Sulfate Reduction (BSR) as was previously proposed, but rather they reflect the contributions of different Fe and S sources during a complex diagenetic history. Pyrite formed from two different mineral precursors: (1) mackinawite precipitated in the water column, and (2) greigite formed in the sediment during early diagenesis. The in-situ analytical approach reveals a complex history of the pyrite nodule growth and allows us to better constrain environmental conditions during the Archean.