An approach to coordinated, spatially resolved, in situ carbon isotope analysis of organic matter and carbonate minerals, and sulfur three- and four-isotope analysis of pyrite with an unprecedented combination of spatial resolution, precision, and accuracy is described. Organic matter and pyrite from eleven rock samples of Neoarchean drill core express nearly the entire range of δ13C, δ34S, Δ33S, and Δ36S known from the geologic record, commonly in correlation with morphology, mineralogy, and elemental composition. A new analytical approach (including a set of organic calibration standards) to account for a strong correlation between H/C and instrumental bias in SIMS δ13C measurement of organic matter is identified. Small (2–3 μm) organic domains in carbonate matrices are analyzed with sub-permil accuracy and precision. Separate 20- to 50-μm domains of kerogen in a single ~0.5 cm3 sample of the ~2.7 Ga Tumbiana Formation have δ13C = −52.3 ± 0.1‰ and −34.4 ± 0.1‰, likely preserving distinct signatures of methanotrophy and photoautotrophy. Pyrobitumen in the ~2.6 Ga Jeerinah Formation and the ~2.5 Ga Mount McRae Shale is systematically 13C-enriched relative to co-occurring kerogen, and associations with uraniferous mineral grains suggest radiolytic alteration. A large range in sulfur isotopic compositions (including higher Δ33S and more extreme spatial gradients in Δ33S and Δ36S than any previously reported) are observed in correlation with morphology and associated mineralogy. Changing systematics of δ34S, Δ33S, and Δ36S, previously investigated at the millimeter to centimeter scale using bulk analysis, are shown to occur at the micrometer scale of individual pyrite grains. These results support the emerging view that the dampened signature of mass-independent sulfur isotope fractionation (S-MIF) associated with the Mesoarchean continued into the early Neoarchean, and that the connections between methane and sulfur metabolism affected the production and preservation of S-MIF during the first half of the planet's history.