Rock-derived or petrogenic organic carbon has traditionally been regarded as being non-bioavailable and bypassing the active carbon cycle when eroded. However, it has become apparent that this organic carbon might not be so inert, especially in fjord systems where petrogenic organic carbon influxes can be high, making its degradation another potential source of greenhouse gas emissions. The extent to which subsurface micro-organisms use this organic carbon is not well constrained, despite its potential impacts on global carbon cycling. Here, we performed compound-specific radiocarbon analyses on intact polar lipid–fatty acids of live micro-organisms from marine sediments in Hornsund Fjord, Svalbard. By this means, we estimate that local bacterial communities utilize between 5 ± 2% and 55 ± 6% (average of 25 ± 16%) of petrogenic organic carbon for their biosynthesis, providing evidence for the important role of petrogenic organic carbon as a substrate after sediment redeposition. We hypothesize that the lack of sufficient recently synthesized organic carbon from primary production forces micro-organisms into utilization of petrogenic organic carbon as an alternative energy source. The input of petrogenic organic carbon to marine sediments and subsequent utilization by subsurface micro-organisms represents a natural source of fossil greenhouse gas emissions over geological timescales.