For finding more sustainable cropping systems, this study on how the farming system influences the yield and quality of potato tubers was carried out with long-term crop rotation experiment. The long-term five-field crop rotation field trial was established with the following farming system treatments: organic farming system treatments: Org I (organic control), Org II (organic crop rotation with winter cover crops) and Org III (organic crop rotation with winter cover crops and the addition of composted cattle manure); conventional farming system treatments: N0 (conventional system without fertilizers), N50 (conventional system with fertilization, N50P25K95), N100 (conventional system, N100P25K95) and N150 (conventional system, N150P25K95). The average yield (based on 3 trial years) of conventional systems was 25% higher, compared to organic systems. However, in organic systems, the yield was the most stable. The most fluctuating cropping system was the most intensively managed N150. In each trial year, the yield differed statistically and it varied from 4.7 t ha⁻¹ up to 10.9 t ha⁻¹. Org I had the same dry matter yield as the N0 system, where chemicals were used, meaning that using chemicals for plant protection but no fertilizer for growth improvement had no positive effect. In each year, the yield in Org III system was similar to N50 system. Regarding the tubers per plant, there were no differences between farming systems but there was a significant difference between the trial years. The tubers in conventional systems had a lower starch content than the organic systems. It is possible to conclude that if cover crops and manure are used, organic farming practices provide just as good results as the conventional farming with low nitrogen level.