Little information is available on pharmaceutical trace compounds degradation pathways in wastewater. The potential of the proteomics approach has been evaluated to extract information on activated sludge microbial metabolism in degrading a trace concentration of a pharmaceutical compound (ibuprofen). Ibuprofen is one of the most consumed pharmaceuticals, measured in wastewater at very high concentrations and, despite its high removal rates, found in different environmental compartments. Aerated and completely mixed activated sludge batch tests were spiked with ibuprofen at 10 and 1,000 μg L−1. Ibuprofen concentrations were determined in the liquid phase: 100% removal was observed and the kinetics were estimated. The solid phase was sampled for proteomics purposes. The first objective was to apply proteomics to evaluate protein profile variations in a complex matrix such as activated sludge. The second objective was to determine, at different ibuprofen concentrations, which proteins followed pre-defined trends. No newly expressed proteins were found. Nonetheless, the obtained results suggest that proteomics itself is a promising methodology to be applied in this field. Statistical and comparative studies analyses provided, in fact, useful information on biological reproducibility and permitted us to detect 62 proteins following coherent and plausible expected trends in terms of presence and intensity change.