There are unusual patterns of greenhouse gas (GHG) net production in soil profiles of Arctic polar deserts. These deserts include frost boils that are symptomatic of permafrost‐associated soils. Some frost boils contain diapirs, intrusions of recently thawed, carbon‐ and water‐rich fine material pushed upward into the overlying active layer. Here we identified diapir‐associated frost boils in an Arctic polar desert that we had previously found to have highly variable patterns of GHG net production, and compared patterns of GHG net production in soil profiles between diapir and non‐diapir frost boils. In addition, we tested the repeatability of soil gas probes measurements and if estimates of diffusivity based on bulk density were accurate. Probes were installed in frost boils identified as including or not including diapirs, and measurements were conducted over several days to evaluate net GHG production.<br/>Soil gas probes deployed for longer than approximately 3 d showed loss of signal, and the injection of an inert tracer, SF₆, validated our estimates of soil diffusivity based on bulk density. Diapir‐associated frost boils showed reduced soil respiration compared with non‐diapir frost boils, despite these diapir‐associated frost boils having increased soil organic matter content. Thus, diapir intrusions in frost boils of the Arctic polar desert simultaneously store greater amounts of organic C and reduce soil respiration compared with non‐diapir frost boils. Differences in soil organic matter quality and/or its interaction with soil texture may be an important control for carbon storage in Arctic soils.