Membrane protein (MP) complexes play key roles in all living cells. Their structural characterisation is hampered by difficulties in purifying and crystallising them. Recent progress in electron microscopy (EM) have revolutionised the field, not only by providing higher-resolution structures for previously characterised MPs but also by yielding first glimpses into the structure of larger and more challenging complexes, such as bacterial secretion systems. However, the resolution of pioneering EM structures may be difficult and their interpretation requires clues regarding the overall organisation of the complexes. In this context, we present BAmSA, a new method for localising transmembrane (TM) regions in MP complexes, using a general procedure that allows tagging them without resorting to neither genetic nor chemical modification. Labels bound to TM regions can be visualised directly on raw negative-stain EM images, on class averages, or on three-dimensional reconstructions, providing a novel strategy to explore the organisation of MP complexes. Display omitted •Transmembrane regions in low and medium-resolution models of membrane proteins are currently identified by indirect means.•Monovalent Streptavidin bound to biotin molecules on biotinylated amphipols/protein complexes was visualised by EM.•Two protocols were used to label successfully the membrane region of both cytochrome bc1 and CsgG with different yields.•mSA particles were visualised by negative stain-EM on raw images, class averages and/or three-dimensional reconstructions.