The permafrost organic carbon (OC) inventory is becoming increasingly vulnerable with ongoing climate warming. Deep thaw processes such as thermokarst development can mobilize organic matter (OM) down to tens of meters deep, allowing microbial decomposition. Respiration rates from thawing permafrost are uncertain, as they depend on geochemical, microbial and ecological parameters. We analysed two 17-m-long sediment cores from below thermokarst lakes in Yakutia, Russia: one from a young upland Yedoma lake and one from an Alas lake formed in a Holocene basin. We carried out one-year-long anaerobic incubations at 4°C and measured GHG production biweekly. In addition, we measured the dissolved OC (DOC) content, as well as n-alkanes concentrations. After one year, the cumulative GHG production was highest in the Yedoma lake core. The higher CO2 production in the still frozen sediments indicates that the labile OM was preserved here. The highest CH4 production in the talik sediments suggests that methanogenic communities have established upon thaw. OM decomposition during previous thermokarst lake formation likely explains the lower GHG production in the Alas lake sediments. We found that CO¬2 production was highest in samples with a high DOC content and a low n-alkane average chain length (ACL). Hence, these parameters likely represent a more labile OM fraction. Our parameters could not explain the CH4 production. We present novel insights that are relevant for mineral-dominated, ice-rich permafrost deposits vulnerable to thermokarst lake formation.