The occurrence of emerging organic contaminants, such as pharmaceuticals, is a growing global concern. In this research, for a membrane bioreactor (MBR) laboratory plant operating at a hydraulic retention time (HRT) of 24 h, fed with real urban wastewater, the heterotrophic biomass behaviour was analysed for two concentrations of erythromycin, ibuprofen, and diclofenac. The concentrations studied for the first phase were erythromycin 0.576 mg L−1, ibuprofen 0.056 mg L−1, and diclofenac 0.948 mg L−1. For Phase 2, the concentrations were increased to erythromycin 1.440 mg L−1, ibuprofen 0.140 mg L−1, and diclofenac 2.370 mg L−1. Heterotrophic biomass was affected and inhibited by the presence of pharmaceutical compounds in both phases. The system response to low concentrations of pharmaceutical compounds occurred in the initial phase of plant doping. Under these operating conditions, there was a gradual decrease in the concentration of mixed liquor suspended solids and the removal of chemical oxygen demand of the system, as it was not able to absorb the effect produced by the pharmaceutical compounds added in both phases.