Autotransporters are a large family of bacterial virulence factors that are defined by a specific domain architecture and transmembrane topology. An N-terminal signal peptide directs secretion of the protein across the inner membrane, and a domain composed of a 12-stranded β-barrel is then folded in a process that entraps segments of a passenger domain, which is the biologically functional portion of the autotransporter molecule. Once translocated and folded into their biologically functional forms, some passengers are autocatalytically processed from their β-barrels and released into the environment to function as toxins, or in disruption of the host immune response. Autocatalysis occurs between two conserved asparagine residues found within an intra-barrel α-helical segment that connects both domains. The α-helix also acts as a plug to block the β-barrel pore post passenger translocation. Immediately downstream of the α-helix is a 10 amino acid unstructured linker region of unknown function. Using biochemical and biophysical assays, we show that the linker region plays an indirect role in autocatalysis, perhaps by ensuring that the α-helix is correctly positioned in the β-barrel lumen. This work demonstrates a previously unrecognised role of the linker region in autotransporter assembly.