A unique miniature membrane bioreactor (mMBR) was designed and applied to examine the biodegradability of two complex organic compounds belonging to a family of brominated flame retardants (BFR) under continuous culture conditions using a bacterial consortium. BFRs are a widely used group of anthropogenic environmental contaminants. Many of these compounds are toxic, persistent, have limited biodegradability, and tend to bioaccumulate in the environment. Their widespread production and use combined with the inappropriate treatment and disposal of industrial wastewater have caused myriad global health and environmental concerns. Dibromoneopentyl glycol (DBNPG) and tribromoneopentyl alcohol (TBNPA) are aliphatic BFRs, classified as recalcitrant compounds, having half-lives of more than 100 years. Following successful debromination and complete biodegradation of the two target compounds in the mMBR, we used molecular and bioinformatic techniques to track changes in bacterial community composition during the biodegradation process.