In animal pathogens, assembly of the type III secretion system injectisome requires the presence of so-called pilotins, small lipoproteins that assist the formation of the secretin ring in the outer membrane. Using a combination of functional assays, interaction studies, proteomics and live-cell microscopy, we determined the contribution of the pilotin to assembly, function and substrate selectivity of the T3SS and identified potential new downstream roles of pilotin proteins. In the absence of its pilotin SctG, Yersinia enterocolitica forms few, largely polar injectisome sorting platforms and needles. In line, the majority of export apparatus subcomplexes is mobile in these strains, suggesting the absence of fully assembled injectisomes. Remarkably, the export of late T3SS substrates including the virulence effectors is hardly affected in these bacteria, whereas early T3SS substrates, such as the needle subunits, are only exported to a very low degree. We found that pilotins transiently interact with the secretin and the large export apparatus component SctV, but mostly localize throughout the bacterial membrane, where they form transient mobile clusters, which do not colocalize with assembled injectisomes. In addition, pilotins interact with non-T3SS components, including sugar transporters. Pilotins therefore have additional functions downstream injectisome assembly, which include the regulation of type III secretion and a potential new link to the cellular energy metabolism.