Membrane bioreactors (MBRs) are known for producing high quality effluent from wastewater treatment facilities in order to meet stringent regulatory requirements (Fleischer et al., 2005), accommodate growth (Vadiveloo & Cisterna, 2008), provide opportunities for water reuse (Schmidt et al., 2011), and achieve other operational goals for various municipalities, utilities and industries (Cummings & Frenkel, 2008). The process of testing, starting up and optimizing an MBR process for enhanced nutrient removal at the end of a construction project is often overlooked. Even a well-designed MBR can fail to meet expectations if the system is not properly configured during the startup phase, making this a critical step in any successful implementation of membrane technology. The startup phase of two municipal MBR plants were compared to demonstrate the importance of various strategies for initial process optimization, with a focus on lessons learned, techniques and performance expectations that can be applied to future projects.