Pharmaceutical compounds such as non-steroidal anti-inflammatory drugs (NSAIDs) and antibiotics have been detected in sewage treatment plant (STP) effluents, surface and ground water and even in drinking water all over the world, and therefore have developed as compounds of concern. Membrane bioreactor (MBR) treatment has gained significant popularity as an advanced wastewater treatment technology and might be effective for an advanced removal of these pollutants. This paper evaluates the treatment of wastewater containing three NSAIDs (acetaminophen, ketoprofen and naproxen) and three antibiotics (roxithromycin, sulfamethoxazole and trimethoprim) performed in two MBRs with sludge retention times (SRTs) of 15 (MBR-15) and 30 (MBR-30) days over a period of four weeks. It was observed that NSAIDs were removed with higher efficiencies than the antibiotics for both MBRs, and the MBR-30 presented higher removal efficiencies for all the compounds than obtained by MBR-15. Removal rates ranged from 55% (sulfamethoxazole) up to 100% (acetaminophen, ketoprofen). Besides mineralisation biological transformation products of ketoprofen and naproxen produced by wastewater biocoenosis were identified in both MBR permeates using liquid chromatography coupled with mass spectrometry (LC-MS). The results indicated the importance of investigating the environmental fate of pharmaceuticals and their transformation products reaching the environment.