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Permafrost thaw leads to thermokarst lake formation and talik growth tens of meters deep, enabling microbial decomposition of formerly frozen organic matter (OM). We analyzed two 17-m-long thermokarst lake sediment cores taken in Central Yakutia, Russia. One core was from an Alas lake in a Holocene thermokarst basin that underwent multiple lake generations, and the second core from a young Yedoma upland lake (formed ~70 years ago) whose sediments have thawed for the first time since deposition. This comparison provides a glance into OM fate in thawing Yedoma deposits. We analyzed total organic carbon (TOC) and dissolved organic carbon (DOC) content, n-alkane concentrations, and bacterial and archaeal membrane markers. Furthermore, we conducted 1-year-long incubations (4°C, dark) and measured anaerobic carbon dioxide (CO 2 ) and methane (CH 4 ) production. The sediments from both cores contained little TOC (0.7 ± 0.4 wt%), but DOC values were relatively high, with the highest values in the frozen Yedoma lake sediments (1620 mg L -1 ). Cumulative greenhouse gas (GHG) production after 1 year was highest in the Yedoma lake sediments (226 ± 212 µg CO 2 -C g -1  dw, 28 ± 36 µg CH 4 -C g -1  dw) and 3 and 1.5 times lower in the Alas lake sediments, respectively (75 ± 76 µg CO 2 -C g -1  dw, 19 ± 29 µg CH 4 -C g -1  dw). The highest CO 2 production in the frozen Yedoma lake sediments likely results from decomposition of readily bioavailable OM, while highest CH 4 production in the non-frozen top sediments of this core suggests that methanogenic communities established upon thaw. The lower GHG production in the non-frozen Alas lake sediments resulted from advanced OM decomposition during Holocene talik development. Furthermore, we found that drivers of CO 2 and CH 4 production differ following thaw. Our results suggest that GHG production from TOC-poor mineral deposits, which are widespread throughout the Arctic, can be substantial. Therefore, our novel data are relevant for vast ice-rich permafrost deposits vulnerable to thermokarst formation., (© 2021 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)