Crohn's disease (CD) is a type of inflammatory bowel disease (IDB). The endoscopic picture of Crohn's disease includes thickened submucosa, transmural inflammation, fissuring ulceration, and non-caseating granulomas. Intestinal microbiome dysbiosis has been described systematically in patients with IBD. In recent decades it was detailed that , especially adherent-invasive (AIEC) pathotype, has been implicated in the pathogenesis of IBD, including Crohn's disease (Palmela, et al., 2018). In comparison with commensal strains of , AIEC strains have a large adhesive-invasive potential therefore its surface composition is of great interest. We presented a dataset of the membrane proteins of strains isolated from patients with Crohn's disease. From the set of isolated from Crohn's disease patients [2] we chose three isolates with strongest AIEC pathotype. We performed proteome-wide LC-MS analysis of membrane fraction of this isolates after invasion or adhesion-invasion to human intestinal CaCo-2 cell line and prior to this (control). The data including LC-MS/MS raw files and exported MaxQuant search results with fasta files were deposited to the PRIDE repository project accession PXD014250.