Microbacterium sp. strain BR1 is a bacterial strain that recently received attention for its capability to mineralize sulfamethoxazole (SMX) and other sulfonamides. In this study, the survival of Microbacterium sp. in municipal sludge waters was tested in batch experiments to explore optimal process conditions. Inoculation of Microbacterium sp. was subsequently performed in a pilot membrane bioreactor (MBR) operated in two configurations: treating full-scale MBR permeate (post-treatment) and treating raw municipal wastewater. SMX removal by Microbacterium sp. could not be proved in any of the configurations, except for SMX concentrations far higher than the ones normally found in municipal wastewater. By use of molecular tools (fluorescence in situ hybridization analysis) a low capability to survive in activated sludge systems was assessed. After inoculation, Microbacterium sp. was reduced to a small fraction of the viable biomass. The observed growth rate appeared to be many times lower than the one of typical activated sludge micro-organisms. Possibilities of application in full-scale municipal wastewater treatment are scarce.