Membrane bioreactors (MBRs) have been increasingly implemented in both small and large-scale wastewater treatment and water reuse schemes. Evaluating persistent compounds and transformation products in these systems is essential for learning how to minimize their input of harmful trace organic chemicals (TOrCs) into the environment. MBRs ability for removing TOrCs has largely relied on targeted or suspect screening approaches for analytical analyses, which can miss potentially important unknown or unexpected chemicals. This research uses a comprehensive two-dimensional time-of-flight mass spectrometry (GC×GC/TOF-MS) based non-targeted approach, to compare an aerobic membrane bioreactor (AeMBR) and an anaerobic membrane bioreactor (AnMBR), operating in parallel, for treating in situ TOrCs in municipal wastewater. The aerobic membrane permeates (AeMP) contained significantly fewer number of chemicals compared to the anaerobic membrane permeates (AnMP), while the number of newly formed compounds were similar between AeMBR and AnMBR, suggesting AeMBR was more effective for removing a wider diversity of compounds. Additionally, AeMP had significantly lower mean peak abundances compared to AnMP. Persistent and removed compounds, and newly formed transformation products unique to AeMP and AnMP were tentatively identified, some of which have not previously been reported in wastewater.