Value of the Data •The dataset contains the first published wide-range proteome analysis of membrane fraction of Escherichia coli isolates from Crohn's disease patients after invasion or after adhesion-invasion to CaCo-2 cell line and prior this. •The data are useful in studies of Crohn's disease or IBD pathogenesis. •These data are valuable for researchers interested in E. coli proteomics. •The data contain three biological and two technical replicates of E. coli culture that allows for extended statistical analysis.