In this paper, it was determined whether and under what conditions walnut shell and cocoa bean extract, obtained from agro-industrial waste, can influence the survival and antioxidant status of cells of the digestive system (tumor epithelial cells of the liver (HepG2), stomach (AGS) and colon cancer) intestines (Caco-2)) and bacterial representatives of the human microbiota (Escherichia coli, Lactobacillus fermentum, Staphylococcus aureus). The influence of the extracts on the change in bacterial adhesion to Caco-2 and Cal-27 cells and the formation of bacterial biofilms was investigated. The daily recommended concentrations of the researched extracts showed a toxic and antioxidant effect on Caco-2 cells, with the fact that the presence of polysaccharides and a longer exposure time enhanced the antioxidant activity of the extracts. The obtained data indicate the antimicrobial character of the extract against the bacterium S. aureus and the ability of the extract to lead to a change in adhesion for the epithelial cells of the digestive system. Polysaccharides played an important role in biofilm formation; walnut shell extract with polysaccharides increased biofilm formation of S. aureus bacteria, while cocoa bean shell extract with polysaccharides decreased biofilm formation of E. coli bacterium.