Ingestion of microplastics can impair nutrition of marine invertebrates. In a laboratory study, we tested whether microplastics affect ingestion rates and gastrointestinal enzyme activities in the marine isopod Idotea emarginata. Isopods were fed for eight days with one out of four different food formulations: natural food (the brown alga Fucus vesiculosus) or synthetic diet consisting of freeze-dried algal powder embedded in agarose, both, with or without microplastic particles (fluorescent polymethyl methacrylate, 10–100 μm) at a concentration of 40 items per mg of food. The isopods accepted both types of food but consumed significantly more (average 3.1-fold) of the agar based synthetic food. I. emarginata responded to the reduced content of digestible organic matter in the synthetic food by a compensatory adjustment of the ingestion rates. Addition of microplastics had no effect on ingestion rates in natural food whereas the feeding rates for synthetic food varied in response to microplastics. Similarly, activity patterns of digestive enzymes, particularly those of esterases, changed significantly in the treatment with synthetic food. Isopods fed with synthetic food alone showed elevated esterase activities in the gut while those isopods fed with synthetic food and microplastics showed elevated esterase activities in the midgut gland but not in the gut. Apparently, not the exposure to microplastic alone, but the combined effects of reduced nutrient availability and microplastic ingestion caused considerable biochemical reactions in the digestive organs of the isopods.