We present 54Fe and 56Fe data on pyrite from burrow-like and irregularly shaped pyrite concretions from Holocene postglacial lacustrine clays in the northern Baltic Sea collected using a secondary ion mass spectrometry (SIMS) microanalysis technique. The burrow-like concretions were formed in reducing, mucus-coated worm burrows in oxic surface sediments. Framboidal pyrite in the cores of the burrow-like concretions shows extensively fractionated δ56Fe values down to −3.1‰. The framboids are cemented by poorly crystalline FeS2 with δ56Fe values between −2.1‰ and +1.4‰. The irregularly shaped concretions with microcrystalline textures were formed in organic-poor sediment pore spaces, and display a wide spread of δ56Fe values up to +4.1‰. The measured δ56Fe values reflect the preferential capture of 54Fe to pyrite in the diagenetic sequence and the 56Fe enrichment of remaining pore water. The diagenetic sequence of the pyrite materials is supported by previous petrographical study and 34S/32S microanalysis of the same samples. Our results demonstrate substantial early-diagenetic δ56Fe and δ34S heterogeneity within individual pyrite grains, underlining the necessity of high spatial resolution measurements in studying biological and abiological isotopic signatures.