Organic carbon (OC) stored in Arctic continental shelf sediment is a climate-sensitive but poorly quantified component of the global carbon cycle. The current interglacial period means that most shelf permafrost, along with its OC, is currently warmer than -2 °C, and therefore susceptible to small additional warming in the near future. Estimating how much OC is potentially stored in subsea permafrost is thus key to a quantitative understanding of potential impacts of permafrost thaw on carbon mobilization in a warming Arctic. We developed a process-based model of permafrost distribution and organic matter (OM) sedimentation and decomposition to estimate the contribution of submarine permafrost to Arctic shelf organic carbon stocks. Driven by Earth System Model forcing, our model calculates 1D heat flow below the earth surface, ice caps and sea bed, and uses a reactivity continuum model of OM decomposition. We restrict our modeling to sediment that was buried within the last four glacial cycles (450 kyr), and therefore neglect OC stocks deeper than about 100 m, including any gas hydrates. Restricting OM decomposition to the liquid habitat for microbial activity in the sediment, we estimated that permafrost below the Arctic Shelf stores at least as much OC as the terrestrial counterpart at pre-industrial time, and probably in the range of twice to three times as much OC. We compared the effect of varying the OC sedimentation rates and OC reactivity. Higher reactivity in marine sediments combined with lower ice contents to increase the rate of OM decomposition, relative to sediment deposited in terrestrial settings. As a result, permafrost in our model preserved a greater proportion of marine OM from decomposition while having little effect (< 5%) on the amount of recalcitrant terrestrial OC. These differences in sedimentation rate and reactivity influence the distribution of OC preservation on the Arctic shelf. Our modeling shows that subsea permafrost is a relevant OC stock and that more research is needed to understand microbial OM decomposition in cold but not necessarily frozen sediments. Given that deeper deposits and gas hydrates are not included, we provide conservative estimates of Arctic shelf OC stocks and suggest that the shelves have acted as long-term carbon sinks over multiple glacial--interglacial cycles.