The integration of β-barrel proteins into the bacterial outer membrane (OM) is catalysed by the β-barrel assembly machinery (BAM). The central BAM subunit (BamA) itself contains a β-barrel domain that is essential for OM protein biogenesis， but its mechanism of action is unknown. To elucidate its function， here we develop a method to trap a native Escherichia coli β-barrel protein bound stably to BamA at a late stage of assembly in vivo. Using disulfide-bond crosslinking， we find that the first β-strand of a laterally 'open' form of the BamA β-barrel forms a rigid interface with the C-terminal β-strand of the substrate. In contrast， the lipid-facing surface of the last two BamA β-strands forms weaker， conformationally heterogeneous interactions with the first β-strand of the substrate that likely represent intermediate assembly states. Based on our results， we propose that BamA promotes the membrane integration of partially folded β-barrels by a 'swing' mechanism.