The ecological situation and modern agro-landscape improvement, soil fertility maintenance and uplifting, formation of ecologically safe agro-ecosystems with germplasm diversity in crop rotation, and cultures-soil conditioners are the focus of the study. Nitrogen is a vital element required in larger quantities by plants; however, lack of it has become a problem in organic farming. The presented study suggests ways organic farming can boost up nitrogen in return to address nitrogen deficiency. The research shows data on the harvest of three-year standing alfalfa and indicators of the efficiency of annual crops’ use in the crop rotation of organic farming. The study findings exhibited that alfalfa accumulates residues of up to 13–17 t ha-1 in three years of standing, containing more than 280–300, 63–80, and 66–120 kg NPK ha-1, respectively. In the efficiency of different crop rotations, the alfalfa accumulated 13 and 20 t ha-1 organic residues in the two- and three-year periods, respectively. More than 11 t ha-1 of green mass containing 65 to 70 kg of nitrogen, 20 to 25 kg of phosphorous, and 55 to 60 kg of potassium accumulates in the soil in welded form. By sowing in good time, mixed with oats, leave the soil with up to 12–15 t of organic matter, containing 190–200, 35–40, and 230–250 kg NPK ha-1, respectively. A pea-oat mixture of about 12.0 t ha-1 of green mass resulted in 132, 46, and 102 kg NPK ha-1, respectively. The latest findings can serve as a basis for the development of new approaches related to the organic farming system in Southeast Kazakhstan.