Two sequencing batch reactors (SBRs) were run to bio-mineralize 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one (NTO) in lab scale settings. The reactors were shown to reproducibly biotransform these munitions under aerobic and anaerobic conditions during the operations of these SBRs. Complete removal (100% biotransformation) of DNAN (initially 17.7 ± 5.4 mg L(-1)) and NTO (initially 15.0 ± 7.1 mg L(-1)) was observed in an anaerobic SBR when Luria-Bertani (LB) broth was present. In contrast, an aerobic SBR degraded only 58 ± 22% of DNAN (initially 19.7 ± 6.2 mg L(-1)) and 45 ± 24% of NTO (initially 9.7 ± 6.3 mg L(-1)) when either LB or glucose was also added indicating that anaerobic conditions are more favorable for biotransformation of these munitions. Transcriptomic analysis of the DNAN and NTO degrading anaerobic SBR revealed upregulation of a putative nitroreductase, hydroxylaminophenol mutases, 4-hydroxylphenyl acetate associated genes, and quinone oxioreductases. Major Bacterial populations included Bacteroidales, Campylobacterales, Enterobacteriales, Pseudomonadales, Burkholderiales and Clostridiales. Results from this study can be used to inform investigation of munition degrading organisms and the functional genes responsible.