Recently, numerous plant-based preparations have been used for health promotion or disease prevention in animals. Chicory is one of the plants that contain various nutraceutics, mainly inulin type fructans (ITFs) showing prebiotic character. In pigs, a significant proportion of ITFs is fermented in the distal part of the small intestine to lactate and short-chain fatty acids (SCFAs). Previous studies have shown that SCFAs are involved in structural rearrangement of the intestinal epithelial mucosa and stimulate intestinal barrier assembly. These changes should be accompanied by a modification of enterocyte protein composition and abundance. Thus, we hypothesized that ITFs, due to their direct or indirect effect, can modify ileal proteome. The experiment was performed on 24 castrated male pigs (PIC × Penarlan P76) assigned to 3 groups (n = 8) fed cereal-based diets: control or experimental: supplemented with 4% of dried chicory root or with 2% of inulin. Mucosa proteins were separated using two-dimensional electrophoresis, followed by the identification of statistically valid proteins with the aid of Matrix Associated Laser Desorption Ionization – Time of Flight mass spectrometry (MALDI-TOF MS). Experimental diets significantly altered expression of proteins involved in: glycolysis/gluconeogenesis, biosynthesis of amino acids, cytoskeleton rearrangement, protein synthesis and processing, cell proliferation and differentiation, and iron absorption. Changes in the expression of proteins associated with energetic metabolism, cell proliferation and cytoskeleton rearrangement may suggest an impact of dried chicory root on the functional maturation of the ileal mucosa. Additionally, changes in transferrin abundance suggest the significance of chicory root and inulin supplementation for intestinal iron absorption.