Carbonaceous nanomaterials (CNMs) can affect agricultural soil prokaryotic communities, but how the effects vary with the crop growth stage is unknown. To investigate this, soybean plants were cultivated in soils amended with 0, 0.1, 100, or 1000 mg kg-1 of carbon black, multiwalled carbon nanotubes (MWCNTs), or graphene. Soil prokaryotic communities were analyzed by Illumina sequencing at day 0 and at the soybean vegetative and reproductive stages. The sequencing data were functionally annotated using the functional annotation of prokaryotic taxa (FAPROTAX) database. The prokaryotic communities were unaffected at day 0 and were altered at the plant vegetative stage only by 0.1 mg kg-1 MWCNTs. However, at the reproductive stage, when pods were filling, most treatments (except 1000 mg kg-1 MWCNTs) altered the prokaryotic community composition, including functional groups associated with C, N, and S cycling. The lower doses of CNMs, which were previously shown to be less agglomerated and thus more bioavailable in soil relative to the higher doses, were more effective toward both overall communities and individual functional groups. Taken together, prokaryotic communities in the soybean rhizosphere can be significantly phylogenetically and functionally altered in response to bioavailable CNMs, especially when soybean plants are actively directing resources to seed production.