Methane is a potent greenhouse gas and some episodes of past global warming appear to coincide with its massive release from seafloor sediments as suggested by carbon isotope records of foraminifera. Here, we present structural, geochemical, and stable carbon isotope data from single foraminiferal calcite tests and authigenic Mg-calcite overgrowths in a sediment core recovered from an area of active methane seepage in western Svalbard at ca. 340 m water depth. The foraminifera are from intervals in the core where conventional bulk foraminiferal δ13C values are as low as −11.3 ‰. Mg/Ca analyses of the foraminiferal tests reveal that even tests for which there is no morphological evidence for secondary authigenic carbonate can contain Mg-rich interlayers with Mg/Ca up to 220 mmol/mol. Transmission electron microscopy (TEM) of the contact point between the biogenic calcite and authigenic Mg-calcite layers shows that the two phases are structurally indistinguishable and they have the same crystallographic orientation. Secondary ion mass spectrometry (SIMS) analyses reveal that the Mg-rich layers are strongly depleted δ13C (δ13C as low as −34.1 ‰). These very low δ13C values indicate that the authigenic Mg-calcite precipitated from pore waters containing methane-derived dissolved inorganic carbon at the depth of the sulfate–methane transition zone (SMTZ). As the depth of the SMTZ can be located several meters below the sediment-seawater interface, interpretation of low foraminiferal δ13C values in ancient sediments in terms of the history of methane seepage at the seafloor must be undertaken with care.