•Nitrogen use efficiency (NUE) decreased in general with increasing N level.•Yield increased from N1 to N2 and changed inconsistently from N2 to N3.•Medium N level (N2) is most suitable from the NUE and yield viewpoints.•Soil type and tillage systems have significant influence on soil physical properties.•Maize and winter wheat yields respond positively to a conservation tillage system. The hypothesis that the optimal nitrogen rate for crop yield and nitrogen use efficiency (NUE) are affected by tillage treatment, crop type and soil properties (type) was evaluated by an experiment which include five different tillage treatments (CT-conventional, SS-subsoiling, CH-chiselling, DH-disk-harrowing and NT-no-till), three levels of nitrogen rates (N1-reduced, N2-optimal and N3-luxury), on two different soil types (Stagnosol and Gleysol) and with two different crops (maize and winter wheat). Soil and plant samples were taken from the first and second year in the second four-year crop rotation cycle. The highest value of soil compaction (ρb-bulk density and PD-packing density) as well as the lowest soil total porosity (P) was found, on average for all tillage treatments, on Gleysol in both experimental year in the root zone (20–40 cm). At all depths the highest values of ρb and PD were recorded for DH treatment on Gleysol and for soil porosity for NT treatment on Stagnosol. Grain yields, biomass, and harvest index of maize and winter wheat on both soil type respond positively to conservation tillage treatment, but with different significations. Soil cover crop residues were significantly affected by soil treatment and nitrogen fertilization (P < 0.01), and decreasing in the following order: NT > CH > SS > DH > CT on both soil types. The average NUE in general decreased successively under N1, N2 and N3 with respective NUEs on Stagnosol 58.5, 49.5 and 36.0 kg kg−1 for maize and 59.9, 45.3 and 35.9 kg kg−1 for winter wheat. Corresponding values on Gleysol were 78.5, 69.4, 52.0 kg kg−1 and 46.3, 51.3, 44.0 kg kg−1. The grain and biomass of winter wheat increased from N1 to N2, whereas from N2 to N3 they decreased, increased or remained almost the same depending on the tillage system and soil type. The effect of all the investigated tillage treatments on NUE and crop yield was variable depending on particular tillage system, crop type and soil type. The results indicate that, from the NUE and crop yield viewpoints, the N2 and N3 nitrogen rates are respectively most and least suitable on both soil types, depending on soil treatment. Irrespective of the nitrogen application rate and tillage treatments, the NUEs were the most comparable treatments higher in the more productive Gleysol (32.7–92.5 kg kg−1) than in Stagnosol (26.4-76.7 kg kg−1).