Arctic lowland tundra is characterized by pronounced spatial heterogeneity that introduces uncertainty into predictions of permafrost soil carbon dynamics. In these ecosystems, edaphic variability is primarily structured along two spatial axes: ice wedge polygon microtopography at the terrain scale and soil layers at the pedon scale. Here, we investigated how polygon types (low-, flat-, and high-centered polygons) and major soil layers (organic topsoil, mineral subsoil, cryoturbated material, and upper permafrost) jointly shape soil organic matter pools, microbial community composition, and potential extracellular enzyme activities. Polygon-specific patterns in soil organic matter characteristics and microbial communities persisted across all soil layers, and soil-layer specific differences were consistent across polygon types, while interactive effects were comparatively minor. Low centered polygons showed reduced organic matter bioavailability, lower microbial abundances, and diminished hydrolytic enzyme potential compared to flat- and high-centered polygons. Organic topsoils emerged as pronounced microbial and enzymatic hotspots. The upper permafrost contained substantial amounts of relatively undecomposed organic matter and indicated a considerable potential for hydrolytic degradation upon thaw. Across both spatial axes, patterns in soil organic matter pools, and microbial communities were largely structured along gradients in organic matter inputs and redox conditions, which themselves arise from interactions in surface microtopography, hydrology, and vegetation. Overall, our findings demonstrate that a limited number of spatial units captures a disproportionate share of edaphic, microbial, and biogeochemical variability in Arctic lowland tundra soils. Explicitly accounting for polygon morphologies and major soil layers therefore provides a tractable framework for upscaling soil processes across spatially heterogeneous ecosystems and improving climate-relevant biogeochemical projections.