Eastern subterranean termite, Reticulitermes flavipes (Kollar), workers were continuously exposed to one of five chitin synthesis inhibiting (CSI) active ingredients and the protist community from the hindgut quantified biweekly for 21 d. The CSIs tested included commercially available formulations of diflubenzuron, hexaflumuron, lufenuron, noviflumuron, and novaluron. Results showed termites exposed to CSIs had a significant decrease (≥30%) in the estimated total protist population after 3 d, regardless of treatment. Protist species impacted were Dinenympha fimbriata, D. gracilis, Microjoenia fallax, Pyrsonympha vertens, and Trichonympha agilis and could be indicative of weakened digestive homeostasis, but further studies are needed. We also provide evidence that lufenuron is highly toxic and discuss some of the implications this might have on termite management practices.