The origin and expansion of biomineralization in eukaryotes played a critical role in Earth history, linking biological and geochemical processes. However, the onset of this phenomenon is poorly constrained due to a limited early fossil record of biomineralization. Although macroscopic evidence for biomineralization is not known until the late Ediacaran, we here report biologically controlled phosphatic biomineralization of scale microfossils from mid-Neoproterozoic (pre-Sturtian) strata of northwest Canada. Primary biological control on mineralization is supported by the identification of apatite in both chert-hosted and limestone-hosted specimens, the conspicuously rigid original morphology of the scale microfossils relative to co-occurring organic-walled cyanobacteria and acritarchs, and the microstructure of the constituent phosphate. Cell-enveloping mineralized scales occur in a wide range of extant protists, but the apparent restriction of phosphate scales to one modern taxon of green algae suggests a possible affiliation for these fossils. Documentation of primary phosphate biomineralization in Fifteenmile Group (Yukon Territory, Canada) microfossils greatly extends the known record of biologically controlled mineralization and provides a unique window into the diversity of early eukaryotes.