Biogas production from manure and other organic matter, or combinations thereof, is part of the circular economy, and the use of the digestate from biogas production for plant nutrition and thus for soil fertility restoration and organic carbon (C) sequestration completes the circular economy cycle. The use of digestate from biogas production in agriculture is one of the sustainable ways to manage manure or organic waste, an alternative to conventional chemical fertilizers, and a means to achieve the objectives of the European Green Deal. To this end, two two-factor pot experiments were carried out in 2019–2020. Factor A—1. Control (without fertilization), 2. Liquid cow manure 170 kg ha−1 N (N170), 3. Digested manure 170 kg ha−1 N (N170), 4. Digested manure 140 kg ha−1 N (N140), 5. Digested manure 110 kg ha−1 N (N110); Factor B—1. Plants not cultivated, 2. Plants cultivated. The experiments determined the effect of digestate on the changes in soil nitrate (NO3-N), ammonium (NH4-N) and mineral (NO3-N + NH4-N) nitrogen, and available phosphorus (P2O5) and potassium (K2O) in the soil without plants as well as with plants cultivated and evaluated the risk of migration of macronutrients into deeper soil layers. The results showed that the application of the highest allowed rates under the Nitrates Directive (N170) and N140 digestate is accompanied by the addition of high levels of ammonium (NH4-N) nitrogen, which alters the balance of ammonium (NH4-N) and nitrate (NO3-N) nitrogen in the soil, and the extent of their migration to the deeper layers. These results suggest that the application of digestate to agricultural land enhances the migration of nitrogen and, in phosphorus-rich soils, of phosphorus (PO4-P) compounds to deeper layers (>25 cm). In order to achieve environmental objectives, digestate rates should be based on the agrochemical properties of the soil and the needs of the plants and should not exceed 65% of the nitrogen needed by the plants from mineral fertilizers.