Integrated petrography, mineralogy, geochronology and geochemistry of cold seep carbonate crusts and free gas from the Alvheim channel elucidate diagenetic carbonate precipitation and related seepage histories in the central North Sea. Free gas isotope characteristics coupled with carbonate δ13C values as low as −66‰ VPDB, indicate a predominantly microbial methane source with minor thermogenic contribution. We estimate that ~70% of the carbon sequestered into carbonate precipitates was derived from local oxidation of methane. The early stage of crust growth is represented by microcrystalline aragonite and Mg-calcite (10 to 40% mol MgCO3) cementing seafloor sediments consisting of clays, quartz, feldspar, and minor detrital low Mg-calcite and dolomite. Typical association of aragonite cement with coarse-grained detritus may reflect elevated fluid flow and flushing of fine particles prior to cementation close to the seafloor. Middle rare earth element enrichment in early generation microcrystalline cements containing framboidal pyrite indicates diagenetic precipitation within the zone of anaerobic methane oxidation contiguous to iron reduction. The later generation diagenetic phase corresponds to less abundant radial fibrous and botryoidal aragonite which lines cavities developed within the crusts. In contrast to early generation cements, late generation cavity infills have rare earth elements and Y patterns with small negative Ce anomalies similar to seawater, consistent with carbonate precipitation in a more open, seawater dominated system. Aragonite U–Th ages indicate carbonate precipitation between 6.09 and 3.46kyr BP in the northern part of the channel, whereas in the southern part precipitation occurred between 1.94 and 0.81kyr BP reflecting regional changes in fluid conduit position. Display omitted •Approximately 70% of carbon in carbonates is derived from microbial methane carbon.•Distinct REY patterns differ with carbonate phases rather than mineralogy.•U–Th ages constrain two distinct seepage events between 6.1 and 0.8ka BP.•Late generation aragonites correspond to carbonate hosted methanotrophy.