Campylobacter jejuni is one of the leading causes of acute gastroenteritis in the developed world, and a major antecedent for a number of debilitating autoimmune disorders. Recently, the serine peptidase Cj0511 has been identified as being required for optimum virulence and is associated with number of virulence mechanisms including biofilm formation, stress tolerance and pancreatic amylase triggered α-dextran secretion. As a component of outer membrane vesicles, which are a key mechanism for delivery of a number of classical mediators of pathogenicity including components into host cells, there is also an implication that Cj0511 may also modify host proteins during infection. Here, we employed iTRAQ-based labelling to determine the effect of loss of the peptidase on whole protein abundance in a hypermotile population of the original sequenced strain; C. jejuni strain 11168H. Of the 1306 C. jejuni proteins quantified, only 67 were deemed to have a significant change in abundance in the Δcj0511 strain relative to the wild-type isolate. Of these, 41 were reverted to WT levels in a complemented strain, Δcj0511Ωcj0046 including a number of proteins from the dccRS regulon, flagellar components and protein secretory systems all of which have known associations with virulence. N-terminal amine isotopic labelling of substrates (N-TAILS) was also employed for a pair wise comparison of the N-degradome of wild-type 11168H and the cj0511 knock out strain to both identify biological targets of the protease as well as attempt to elucidate the sequence specificity of the protease. These proteomics-based approaches were complemented with various standard phenotypic tests to further establish the role of the protease towards C. jejuni’s physiology.