Bacterial lipoproteins are surface exposed, anchored to the membrane by S diacylglyceryl modification of the N-terminal cysteine thiol. They play important roles in many essential cellular processes including, in bacterial pathogens, at the host-pathogen interface. Clostridium difficile is a Gram-positive anaerobe that causes severe gastrointestinal disease. Its lipoproteome remains poorly characterized, but is likely to be important in colonization of the host and in transmission of infection. This dataset utilised metabolic tagging with alkyne-tagged lipid analogues, followed by click ligation to biotin and affintiy enrichment, in combination with diemthyl albelling based quantitative proteomics to profile protein lipidation across diverse C. difficile strains. Additionally, the lipoproteomes of mutants inactivated in specific components of the lipoprotein biogenesis pathway and a mutant in the spo0A gene are included. For all strains a complementary global proteome is provided, split into soluble and insoluble fractions and quantifed by dimethyl labelling.