Current processes to manufacture nanotubes at commercial scales are unfortunately imperfect and commonly generate undesirable byproducts. After manufacturing, purification is necessary and is a rate and cost determining step in advancing the development of commercial products based on nanotubes. Boron nitride nanotubes (BNNTs) produced without metal catalysts from high-temperature processes are known to contain a significant amount (e.g., 50 wt %) of various boron derivatives. Herein we report a simple yet efficient and scalable process to purify these types of BNNT materials at commercial scales, from a few grams to hundreds of grams, at purity over 85 wt % in a single step. The process relies on a vertically mounted flow tube reactor and scrubber system that can be operated under pure or diluted chlorine gas flow at temperatures up to 1100 °C. The main chemical reactions driving the purification are the conversion of boron and BN derivatives into BCl3 and HCl, which are removed as gaseous species, while pristine BNNTs are left behind. The preferential etching of impurities over pristine BNNTs shows the extreme chemical resistance of BNNTs in this harsh environment and opens up new applications for this nanomaterial. The process has been examined at various temperatures, up to 1050 °C, and the resulting materials display improved BNNT purity and quality across a range of imaging and spectroscopic assessments. The recommended temperature to optimize quality with yield is 950 °C, although higher quality material is obtained at a higher temperature.