The ATP‐binding cassette transporter MsbA is a lipid flippase, translocating lipid A, glycolipids, and lipopolysaccharides from the inner to the outer leaflet of the inner membrane of Gram‐negative bacteria. It has been used as a model system for time‐resolved structural studies as several MsbA structures in different states and reconstitution systems (detergent/nanodiscs/peptidiscs) are available. However, due to the limited resolution of the available structures, detailed structural information on the bound nucleotides has remained elusive. Here, we have reconstituted MsbA in saposin A–lipoprotein nanoparticles (Salipro) and determined the structure of ADP‐vanadate‐bound MsbA by single‐particle cryo‐electron microscopy to 3.5 Å resolution. This procedure has resulted in significantly improved resolution and enabled us to model all side chains and visualise detailed ADP‐vanadate interactions in the nucleotide‐binding domains. The approach may be applicable to other dynamic membrane proteins. [ABSTRACT FROM AUTHOR]