Development of mixed-culture microbial granules under aerobic conditions in a sequencing batch reactor (SBR), capable of completely degrading a recalcitrant metal chelating agent is reported. In laboratory-scale reactor studies, the microbial granules degraded 2 mM of free nitrilotriacetic acid (NTA) and Fe(III)–NTA completely in 14 and 40 h, respectively. Free NTA was degraded at a specific rate of 0.7 mM (g MLSS) −1 h −1, while Fe(III)–NTA was degraded at a specific rate of 0.37 mM (g MLSS) −1 h −1. Achievement of significant degradation rates of NTA and ferric–NTA in double-distilled water suggests that the microbial metabolism is not constrained by lack of essential elements. Efficient degradation of recalcitrant synthetic chelating agents by aerobic microbial granules suggests their potential application in a variety of situations where heavy metals or radionuclides are to be co-disposed with metal chelating agents.