Weathering continuously converts rock to regolith at Earth’s surface while regulating the atmospheric concentrations of CO2 and O2. Shale weathering is of particular interest because shale, the most abundant rock type exposed on continents, stores much of the ancient organic carbon (OCpetro) buried in rocks. Using geochemical and mineralogical analysis combined with neutron scattering and imaging, we investigated the weathering profile of OCpetro in saprock in a black shale (Marcellus Formation) in the Ridge and Valley Appalachians in Pennsylvania, U.S.A. Consistent with the low erosion rate of the landscape, we discovered that Marcellus is completely depleted in carbonate, plagioclase, and pyrite in saprock below the soil layer. On the contrary, only ∼60% of OCpetro was depleted in saprock. By comparing the pore structure of saprock to bedrock and samples combusted to remove organic matter (OM), we confirmed that the large particles of OM are preferentially depleted, leaving elongated pores of tens to hundreds of micrometers in length, while the smaller particulates of OM (ranging from ∼5 to ∼200 nm) are largely preserved during weathering. The retarded weathering of small OM particles is attributed to their close association with mineral surfaces in the shale matrix. The texture of OM in shale is underappreciated as an important factor that controls porosity generation and the weathering rate of OCpetro.