Microdigitate stromatolites (MDS) are common in Neoarchean–Paleoproterozoic successions but declined and gradually disappeared in Meso- and Neoproterozoic carbonates. The abundance of well-preserved fibrous fabrics and the absence of identifiable microbial fossils in MDS have been taken as evidence of their abiotic origin in carbonate-supersaturated and anoxic Precambrian oceans. Micron- and nanometer-scale features of MDS from the Mesoproterozoic Wumishan Formation (ca. 1.45–1.5 Ga) of the North China platform composed of alternating submillimetric dark and light laminasets are morphologically similar to those reported from elsewhere in the geological record. The dark laminasets are micritic and contain abundant fuzzy-edged micropeloids and filaments. The micropeloids are commonly 10–70 µm in diameter and commonly surrounded by thin (<10 µm) rims composed of amorphous micrite or microsparite (some rims now replaced by silica). The filaments are morphologically similar to the bacterial filaments in modern microbialites and contain kerogenous components as indicated by Raman spectrometry analysis. All the laminasets are characterized by fibrous fabrics that are expressed by alternating brown fibers (<10–25 µm) and light microsparitic strips of approximately equal width in transverse direction. Filaments, relics of putative extracellular polymeric substances (EPS), micropeloids, and nanoglobules are closely associated with the brown fibers. These organomineralization-related features suggest a biogenic origin for the MDS of the Wumishan Formation and may have an implication to other MDS from the Neoarchean–Paleoproterozoic successions. Microbially induced micro- and ultrastructures including fibrous fabrics, filaments, micropeloids, and nanoglobules are best preserved in silicified MDS samples, implying that early silicification is critical for the preservation and recognition of organominerals.