Campylobacter jejuni is a Gram-negative microaerophilic bacterium that is the leading cause of food-borne gastroenteritis in developed countries. The common route of human infection is via consumption of poorly prepared or under-cooked poultry, in which C. jejuni is an asymptomatic commensal. Human disease is characterised by mild to severe diarrhoea, vomiting and inflammation. The molecular basis for C. jejuni infection includes initial adherence to, followed by invasion of, human intestinal epithelium. Bacterial peptidoglycan (PG) is an integral component of the cell wall/membrane that is involved in pathogen colonization, host-pathogen interactions, cell structure and morphology. Disruption of PG integrity results in cell lysis making it the major target for existing and novel antibiotics. C. jejuni contains a protein N-glycosylation gene (pgl) cluster that modifies membrane-associated proteins and deletion of genes in this cluster results in reduced pathogenesis. Proteome analysis revealed several glycoproteins in the PG biosynthesis pathway were impacted by oligosaccharyltransferase (pglB) gene deletion. We therefore investigated whether glycosylation influenced the peptidoglycome. Wild type and pglB mutant strain PG structures were isolated and analysed using LC-ESI tandem mass spectrometry. The structural features and relative abundance changes of peptidoglycans in each strain were determined. In addition to the already known peptidoglycans, we discovered several unique structural modifications on the N-acetylneuraminic acid residues and showed that these changes are modulated differently in pglB mutant strains compared to wild-type. The observed variations in the PG structure impacted lysozyme resistance, supporting the role of wild-type PG composition for C. jejuni host survival. In summary, our results show that changes in protein glycosylation impact the structural composition of the PG layer commensurate with changes to PG-associated proteins observed at the proteome level. Unravelling PG structures and the factors involved in their biosynthesis may help in defining why N-glycosylation is critically required for C. jejuni pathogenesis.