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Abstract. Organic matter in Archean hydrothermal cherts may provide an important archive for molecular traces of the earliest life on Earth. The geobiological interpretation of this archive, however, requires a sound understanding of organic matter preservation and alteration in hydrothermal systems. Here we report on organic matter (including molecular biosignatures) enclosed in hydrothermally influenced cherts of the Pleistocene Lake Magadi (Kenya; High Magadi Beds and Green Beds). The Magadi cherts contain low organic carbon (< 0.4 wt %) that occurs in the form of finely dispersed clots, layers, or encapsulated within microscopic carbonate rhombs. Both extractable (bitumen) and non-extractable organic matter (kerogen) were analyzed. The bitumens contain immature “biolipids” like glycerol mono- and diethers (e.g., archaeol and extended archaeol), fatty acids, and alcohols indicative for, inter alia, thermophilic cyanobacteria, sulfate reducers, and haloarchaea. However, co-occurring “geolipids” such as n-alkanes, hopanes, and polycyclic aromatic hydrocarbons (PAHs) indicate that a fraction of the bitumen has been thermally altered to early or peak oil window maturity. This more mature fraction likely originated from defunctionalization of dissolved organic matter and/or hydrothermal petroleum formation at places of higher thermal flux. Like the bitumens, the kerogens also show variations in thermal maturities, which can partly be explained by admixture of thermally pre-altered macromolecules. However, findings of archaea-derived isoprenoid moieties (C20 and C25 chains) in kerogen pyrolysates indicate rapid sequestration of some archaeal lipids into kerogen while hydrothermal alteration was active. We posit that such early sequestration may enhance the resistance of molecular biosignatures against in situ hydrothermal and post-depositional alteration. Furthermore, the co-occurrence of organic matter with different thermal maturities in the Lake Magadi cherts suggests that similar findings in Archean hydrothermal deposits could partly reflect original environmental conditions and not exclusively post-depositional overprint or contamination. Our results support the view that kerogen in Archean hydrothermal cherts may contain important information on early life. Our study also highlights the suitability of Lake Magadi as an analog system for hydrothermal chert environments on the Archean Earth.