Application of nitrogen (N) in contrastive chemical form changes availability of soil nutrients, affecting crop response. This hypothesis was evaluated based on field experiments conducted in 2015/16 and 2016/2017. The experiment consisted of three nitrogen fertilization systems: mineral-ammonium nitrate (AN) (M-NFS), organic-digestate (O-NFS), 2/3 digestate + 1/3 AN (OM-NFS), and N rates: 0, 80, 120, 160; 240 kg ha−1. The content of nitrogen nitrate (N-NO3) and available phosphorus (P), potassium (K), magnesium (Mg) and calcium (Ca) were determined at rosette, onset of flowering, and maturity of winter oilseed rape (WOSR) growth from three soil layers: 0.0–0.3, 0.3–0.6, 0.6–0.9 m. The optimum N rates were: 139, 171 and 210 kg ha−1 for the maximum yield of 3.616, 3.887, 4.195 t ha−1, for M-NFS, O-NFS, OM-NFS. The N-NO3 content at rosette of 150 kg ha−1 and its decrease to 48 kg ha−1 at the onset of flowering was the prerequisite of high yield. The key factor limiting yield in the M-NFS was the shortage of Ca, Mg, O-NFS—shortage of N-NO3. Plants in the OM-NFS were well-balanced due to a positive impact of the subsoil Mg and Ca on the N-NO3 content and productivity. The rosette stage was revealed as the cardinal for the correction of WOSR N nutritional status.