Tomato is a herbaceous one-year plant. It consists of 93-95% water, 5-7% dry matter, organic acids (lemon and apple), sugars (glucose, fructose and sucrose), alcohol-insoluble substances (proteins, cellulose, pectin, polysaccharides), carotenoids and lipids. The aim of this paper was to test the efficacy of microcapsules based on biopolymer alginate with simultaneously encapsulated copper (Cu2 +) or calcium (Ca2 +) and Trichoderma viride fungus spores on the yield and quality of tomatoes grown in soil in protected nonheated greenhouses. During the multiple harvests, the number of marketable and non-marketable fruits, the mass of marketable and non-marketable fruits, yield and qualitative properties was established. Chemical analysis showed the proportion of carotenoids, total polyphenols, and antioxidant activity of fruits. The results showed a positive influence on the tomatoes treated with microcapsules. To distinguish a particular tomato treatment is difficult because, with the genetics of each tomato variety, each treatment showed relatively different results. Treatment with microcapsules with Cu2 + gave the best results in terms of morphological characteristics. Microcapsules loaded with Ca2+ had a positive effect on lycopene content.