Bacterial outer membranes incorporate proteins of at least three well characterized architectures: β-barrel proteins, lipoproteins and secretins. Assembly of β-barrel proteins into the outer membrane is mediated by the β-barrel assembly machinery (BAM) consisting of an essential core β-barrel BamA and four accessory lipoproteins (BamBCDE). Lipoproteins are anchored to the outer membrane by covalently attached lipid modifications and are inserted into the outer membrane by the outer membrane receptor LolB after being translocated across the periplasm by the Lol machinery. Secretins often rely on a small lipoprotein, termed pilotin, to catalyze the efficient translocation of secretin monomers to the outer membrane for assembly into a functional secretion pore. However the mechanism of secretin assembly and the requirement of the BAM complex to assemble non β-barrel proteins into the outer membrane are poorly understood. Using a BamA depletion strain of Escherichia coli, we have designed assays to measure outer membrane protein assembly. Under BamA depleted conditions the levels of outer membrane proteins including autotransporter Ag43 were severely reduced. In contrast GspD, a secretin from a type two secretion system, showed variable dependence on BamA and was able to assemble into mature pores which were integrally inserted into the outer membrane under BamA shut down conditions. These assays provide insight into the role of the BAM complex, and help dissect the mechanisms of protein targeting for assembly within the outer membrane environment.