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Abstract Permafrost thawing is mobilizing dissolved organic carbon (DOC) stored in Arctic frozen soils into rivers, but vertical transport mechanisms within soil columns remain unclear, hindering accurate estimation of soil‐derived DOC export. Through leaching experiments on active‐layer organic soils and underlying mineral permafrost, this study reveals that mineral permafrost exhibits high soil carbon loss as DOC (3.27%–11.42%). However, 11.17%–46.42% of active‐layer DOC is retained by mineral permafrost during vertical transport, forming an internal soil carbon sink. The sink selectively retains aromatic compounds, acting as a molecular “filter” that alters DOC composition and bioavailability. This internal retention complicates interpretations of active‐layer DOC transport dynamics and alters the chemistry of both thawed permafrost and exported DOC. The findings emphasize the critical role of intra‐soil DOC transformations in Arctic carbon cycling.