The aim of our studies was to determine the suitability of organic substrate: peat, coconut fiber with a 20% admixture of chips, and coconut fiber with a 40% admixture of chips (as alternative substrates in relation to rockwool) in intensive horticultural cultures with fertigation adopted as the fertilization method. Tomato was the model plant in this study. Evaluations comprised yielding of plants, contents of macro- and microelements in leaves and fruits, plus changes in the counts of different groups of microorganisms: bacteria, fungi, Actinomycetes, and dehydrogenase activity in the root medium of plants during their vegetation. The significantly highest total yield of plants was found in the case of plants grown in peat and in coconut fiber with a higher (40%) content of chips (9.28 kg·m^-2 each) in relation to rockwool (8.35 kg·m^-2). A similar trend was recorded in the case of commercial yield. Applied substrates significantly modified yielding fruit of grades IVI. Despite the recorded significant modifying effect of the substrate on nutrient contents in leaves and fruits of plants grown in it, no visual symptoms of their deficiencies were observed, which indicates an adequate plant nutrition in both rockwool and organic substrates. Analyzed organic substrates are perfectly suitable for application in intensive culture of vegetables under cover. After the completion of the plants’ cultivation cycle they become valuable organic fertilizer, exhibiting advantageous microbiological parameters, i.e. relatively high counts of fungi, bacteria, and Actinomycetes, as well as dehydrogenase activity, which may improve the fertility of the soil on which they have been utilized.