Campylobacter jejuni is the leading cause of bacterial gastroenteritis in the developed world, with infection is predominantly caused by the consumption of undercooked poultry. C. jejuni exists mainly as a commensal within the intestines of chickens, but is pathogenic in humans. The presence of bile salts in the human intestinal environment play an important role as antimicrobials, and gut pathogens such as C. jejuni often respond strongly to compounds such as deoxycholate, adapting their protein synthesis in an attempt to counteract the toxic effects of these bile salts. As a microaerophilic human pathogen, C. jejuni, particularly the iron‐sulfur clusters found in many of its key enzymes, is susceptible to oxidative stresses posed by its environment, and as such has evolved many proteins dedicated to protecting it against these stresses. In this study, we characterised changes in intracellular protein and metabolite levels of C. jejuni when grown under 0.1% sodium deoxycholate, then validated select protein and metabolite changes using functional assays to describe the altered phenotype induced by exposure to deoxycholate. The results showed a marked decrease in abundance of proteins and metabolites that have known functions in protection against oxidative stress, and a marked increased in abundance of various membrane- and transport-related proteins. Functional validation assays confirmed that growth under deoxycholate greatly sensitised cells to oxidative damage, with cells exposed to the bile salt more than 20 times more susceptible to hydrogen peroxide treatment. This was a specific effect, as deoxycholate did not result in an overall weakened phenotype, with growth in the bile salt increasing adherence and invasiveness of mammalian intestinal cells, motility, and resistance to several antibiotics, consistent with proteomics showing increased abundance of drug transport proteins.