Land colonization by plants and their fungal and bacterial symbionts during the Paleozoic was fundamental to the evolution of terrestrial ecosystems, but how these early communities influenced mineral weathering and soil development remains largely unknown. We investigated cryptogamic ground covers (CGCs) in Iceland to identify modern analogous communities and to characterize soil structure and biologically mediated weathering features. Using a novel application of X-ray microcomputed tomography, we show that moss-dominated CGCs and their soils are not adequate analogues of early communities. Comparisons with the 407 Ma Rhynie Chert (Scotland) biota indicate that modern CGCs dominated by lichens, liverworts, and their associated symbionts (fungi, cyanobacteria) are more representative of early soil-forming communities. Liverwort and lichen soils are thin, and their depth and complexity are constrained by the size and growth form of the dominant plants or lichens. They are aggregated and stabilized by cyanobacteria, mycorrhizal and lichenized fungi, rhizoids, and associated exudates. Smectite was associated with liverwort but not with moss CGC soils. Soil grain dissolution features are diverse and attributable to different organisms (e.g., bacteria, fungi) and types of interaction (e.g., symbiosis). We postulate that such features provide a novel indirect means of inferring biotic interactions in paleosols.