Careless use of plastic products leads to massive litter accumulations in natural environments. Due to the river runoff and gradual degradation of larger plastic pieces into micro-sized particles, microplastics enter to the marine environment. Recently it was demonstrated, that subtidal marine isopods Idotea emarginata, readily ingested and excreted microplastics, without clogging the digestive system. In the present study, we focused on physiological effects of food quality and microplastics, by applying different feeding treatments. Digestive enzymes and protein content in the midgut gland and gut were investigated. Feeding rates differed significantly between natural and artificial diets, but have not changed when microplastics were added to diets. Enzyme activities showed high scatter and inconsistent results. Esterase activity was enhanced in the midgut gland and suppressed in the gut tissue, by microplastics in the agarose. Microplastics further suppressed lipase activity in the midgut of fresh algae fed isopods. Exopeptidase activity was suppressed and endopeptidase enhanced in the midgut gland, due to microplastics in agarose. Microplastics increased protein content of the gut tissue. Our results indicate, that microplastics may differently affect digestive processes of marine isopods. Further research is needed to verify whether these alterations affect nutrient assimilation and nutritional health of the isopods.