New energetic formulations containing insensitive high explosives (IHE), such as 2,4-dinitroanisole (DNAN), 3-nitro-1,2,4-triazole-5-one (NTO), and nitroguanidine (NQ) are being developed to provide safer munitions. The addition of IHE to munitions formulations results in complex wastewaters from explosives manufacturing, load and pour operations and demilitarization activities. New technologies are required to treat those wastewaters. The core objective of this research effort was to develop and optimize a dual anaerobic-aerobic membrane bioreactor (MBR) system for treatment of wastewater containing variable mixtures of traditional energetics, IHE, and anions. The combined system proved highly effective for treatment of traditional explosives (TNT, RDX, HMX), IHE (DNAN, NTO, NQ) and anions commonly used as military oxidants (ClO4−, NO3−). The anaerobic MBR, which was operated for more than 500 d, was observed to completely degrade mg L−1 concentrations of TNT, DNAN, ClO4− and NO3− under all operational conditions, including at the lowest hydraulic residence time (HRT) tested (2.2 d). The combined system generally resulted in complete treatment of mg L−1 concentrations of RDX and HMX to <20 μg L−1, with most of the degradation occurring in the anaerobic MBR and polishing in the aerobic system. No common daughter products of DNAN, TNT, RDX, or HMX were detected in the effluent. NTO was completely transformed in the anaerobic MBR, but residual 3-amino-1,2,4-triazole-5-one (ATO) was detected in system effluent. The ATO rapidly decomposed when bleach solution was added to the final effluent. NQ was initially recalcitrant in the system, but microbial populations eventually developed that could degrade >90% of the ∼10 mg L−1 NQ entering the anaerobic MBR, with the remainder degraded to <50 μg L−1 in the aerobic system. The dual MBR system proved to be capable of complete degradation of a wide mixture of munitions constituents and was resilient to changing influent composition.