The aim of investigation conducted in the years 2009-2011 was to determine the influence of irrigation and effective microorganisms on quantity of main crops (tubers, grain, seeds) and side-line crops (straw) and chemical composition of crops (content of total nitrogen, phosphorus, potassium, magnesium, calcium, copper, iron, manganese, zinc and boron) of the plants species cultivation in organic crop rotation on light soil. The crop rotation contained following agricultural plant species: potato, rye, oat, buckwheat, yellow lupine. This experiment considered four combinations: irrigated (N), irrigated + effective microorganisms (N + EM), non-irrigated (NN), non-irrigated + effective microorganisms (NN + EM). Drip irrigation method (potato) and spray irrigation method (different species plants) was applied in this experiment. The effective microorganisms in form of EM Farming and Humobak in spring were applied and mixed with soil. Significant differences for quantity of main and side-line crops among cultivation plants species were stated, but there were not significant differences regarding research combinations. Significant differences content of nitrogen, phosphorus, copper and manganese in relationship to main crops between combinations and plants species were found, but for of potassium, magnesium, calcium, zinc, boron and iron only between plants species. For side-line crops significant differences content of macro- and microelements between plants species were stated.