Seafloor methane seepage is a significant source of carbon in the marine environment. The processes and temporal patterns of seafloor methane seepage over multi-million-year time scales are still poorly understood. The microbial oxidation of methane can store carbon in sediments through precipitation of carbonate minerals, thus providing a record of past methane emission. In this study, we compiled data on methane-derived carbonates to build a proxy time series of methane emission over the last 150 My and statistically compared it with the main hypothesised geological controllers of methane emission. We quantitatively demonstrate that variations in sea level and organic carbon burial are the dominant controls on methane leakage since the Early Cretaceous. Sea level controls methane seepage variations by imposing smooth trends on timescales in the order of tens of My. Organic carbon burial is affected by the same cyclicities, and instantaneously controls methane release because of the geologically rapid generation of biogenic methane. Both the identified fundamental (26-27 My) and higher (12 My) cyclicities relate to global phenomena. Temporal correlation analysis supports the evidence that modern expansion of hypoxic areas and its effect on organic carbon burial may lead to higher seawater methane concentrations over the coming centuries.