Si nanocrystals (NCs) are synthesizable in low-pressure plasmas with narrow diameter distributions because of unipolar negative charging in the plasma. However, NCs must pass into a spatial afterglow, where NCs may decharge and aggregate. We use both low-pressure differential mobility analysis and quantitative TEM image analysis to examine Si NCs sampled from a 2 Torr Ar-SiH4 plasma reactor. We find that Si NCs are incorporated into aggregates largely composed of 20 and fewer primary particles with nearly equal concentrations of negatively and positively charged NCs. The projected areas of aggregates scale with aggregate volume in similar manner to the scaling observed for aggregates from atmospheric pressure systems. Higher aggregate concentration is observed with increasing flow rate, while larger aggregate size is found with increasing precursor concentration. Measurements show that the spatial afterglow has a significant influence on the charge and extent of NC aggregation. (C) 2020 Elsevier B.V. All rights reserved.