Lipid interactions modulate the function, folding, structure, and organization of membrane proteins. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has emerged as a useful tool to understand the structural dynamics of these proteins within lipid environments. Lipids, however, have proven problematic for HDX-MS analysis of membrane-embedded proteins, due to their presence impairing proteolytic digestion, causing liquid chromatography column fouling, ion suppression, and/or mass spectral overlap. Here, we describe the integration of a chromatographic phospholipid trap column into the HDX-MS apparatus to enable online sample delipidation prior to protease digestion of deuterium labeled protein-lipid assemblies. We demonstrate the utility of this method on membrane scaffold protein lipid nanodisc – both empty and loaded with the ~115 kDa transmembrane protein AcrB – proving efficient and automated phospholipid capture with minimal D-to-H back-exchange, peptide carry-over, and with minimal protein loss. Our results provide insights into the efficiency of phospholipid capture by ZrO2-coated and TiO2 beads, and describe how solution conditions can be optimized to maximize the performance of our online, but also the existing offline, delipidation workflows for HDX-MS. We envision that this HDX-MS method will significantly ease membrane protein analysis, allowing to better interrogate their dynamics in artificial lipid bilayers or even cell membranes.