Petrochemical wastewater treatment is a new sector for the possible widespread application of membrane bioreactor technology. In this field, hard to degrade compounds such as amines and nitrogen residuals were generally the major issues. In addition, over the last years the irregular operation of the manufacturing plants involved drastic variability of the wastewater’s loadings and characteristics, so as to call for more flexible schemes of the treatment plants. This paper compares two different schemes of a continuously fed membrane bioreactor to adequate the nitrification potential to the influent loadings. These are: a) controlled and continuous external ammonia dosage; b) sequencing batch nitrifier enrichment. On the basis of lab and pilot-scale treatment of real petrochemical wastewater, the cyclic batch enrichment process proved to be reliable, cost-effective, and easy to control, being more flexible with respect to changeable influent loadings.