Protein glycosylation in Helicobacter pylori is known to modify the flagellins with pseudaminic acid (pse). This modification is required for proper flagellum production and H pylori motility, which implicates protein glycosylation in H. pylori’s pathogenesis. We investigated whether protein glycosylation extends beyond pse-specific flagellin glycosylation by the use of H pylori pse biosynthesis mutants and the detection of glycoproteins by glycoprotein-specific chemical labelling. Using these methods, we demonstrated the presence of novel protein glycosylation in H pylori, in terms of both the identification of membrane glycoproteins and at least two alternative glycosylation pathways. In addition, a link between protein glycosylation and lipopolysaccharide (LPS) biosynthesis was elucidated, in which the O-antigen ligase, WaaL, is a candidate glycoprotein and was shown to exhibit general oligosaccharyltransferase activity. Overall, this study highlights that protein glycosylation affects several proteins in H pylori and has a key role in the production of multiple virulence factors