The 1.88-billion-year-old Gunflint carbonaceous microfossils are renowned for their exceptional morphological and chemical preservation, attributed to early and rapid entombment in amorphous silica. The carbonaceous matter lining and partly filling filamentous and spherical structures is interpreted to be indigenous, representing thermally altered relicts of cellular material ( kerogen). Here we show that stromatolitic black cherts from the Gunflint Formation, Schreiber Beach, Ontario, Canada, were saturated in syn-sedimentary oil. The thermally altered oil (pyrobitumen), which occurs in the stromatolites and intercolumn sediments, fills pores and fractures, and coats detrital and diagenetic grain surfaces. The occurrence of detrital bitumen grains in the stromatolites points to the proximity of shallow seafloor oil seeps and hence the possible existence of chemosynthetic microbes degrading hydrocarbons. We suggest that hydrocarbons that migrated through the silicifying stromatolites infiltrated semi-hollow microbial molds that formed following silica nucleation on the walls or sheaths of decayed cells. Upon heating, the hydrocarbons were transformed to nanoporous pyrobitumen, retarding silica recrystallization and enhancing detailed preservation of the carbon-rich microfossils. Hydrocarbon infiltration of silicified microbes offers a new explanation for the preservation of the Gunflint microfossils and may have played a role in the formation of some of Earth's oldest microfossils.