Tomato is a vegetable species with long growing period and high needs for plant nutrients. Although soilless grown plants are supplied with readily available nutrients, symptoms of deficiency and physiological disorders are possible. Since the positive effect of biopolymer microcapsules in such cases is known, a study was conducted to determine the effect of the microcapsules with encapsulated copper or calcium ions and their combination with Trichoderma fungus application on the yield and quality of hydroponically grown tomatoes. The cultivars 'Abellus', 'Alamina', 'Clarabella' and 'Vasanta' were tested. During the multiple harvests, the number and weight of marketable fruits, the share of non-marketable fruits, the marketable yield and the qualitative characteristics were determined. The chemical analysis determined the share of lycopene, total polyphenols and antioxidant activity. Cultivars differed significantly in the yield components observed, while microcapsule treatments showed a positive effect compared to untreated control. The use of calcium ion capsules in most of the tested cultivars had a positive effect on the observed quality parameters, which has been expected due to the important role of calcium in the plant.