The aim of this study was to evaluate the impact of ethanol extracts from sea buckthorn and Cornelian cherry fruits and leaves on physiology of gastrointestinal tract cells. We used three cell lines relevant to the types of cells, which are exposed to bioactive compounds after oral administration, namely intestinal absorptive cells (Caco-2/HT-29 MTX model), hepatocytes (HepG2 cells) and immunocompetent cells (RAW 264.7 and P388D1 monocytes). The contents of antioxidant and bioactive polyphenols, such as cinnamic, caffeic and p-coumaric acids, rutin, myricetin, resveratrol, quercetin, apigenin and kaempferol, were assessed in the extracts using HPLC chromatography. The application of the extracts to Caco-2/HT-29-MTX cultures increased enterocyte differentiation markers (alkaline phosphatase and villin1 level) and goblet cell markers (mucins) over a fortnight. The extracts reduced lipid droplet size in hepatocytes challenged with hyperglycaemic glucose concentration, insulin and palmitate. Sea buckthorn leaf, fruit and Cornelian cherry leaf extracts blocked oxidative burst in the PMA-stimulated monocytes, while the sea buckthorn leaf and Cornelian cherry fruit extracts downregulated lipopolysaccharide-induced NO and IL-1β, respectively. The results indicate that the tested extracts modulate the behaviour of cells in the gastrointestinal tract in a beneficial way, especially regarding lipid accumulation and innate immunity actions.