In organic farming, nutrient cycling is based mainly on a farm level with external inputs only when organic fertilisers are not cycled and produced, and conventional systems largely depend on external inputs. Therefore, crop rotations are important tools for maintaining soil fertility and for increasing crop yields and qualities not only in organic farming systems but also in conventional systems. Moreover, proper nutrient management is a key element for sustainable farming. To identify the farming systems that would be sustainable for a longer period, a field experiment was conducted. The aim of this study was to investigate how different farming systems influenced tuber yields and quality (N, NO3−, P, K, Ca, Mg, dry matter and starch concentrations) of potato as well as how potato cultivation within a crop rotation under different farming systems affects soil quality (pH, Ntot, Corg, plant available P, K, Ca and Mg concentrations). Potato (Solanum tuberosum L.) was part of a five crop rotation experiment in which red clover (Trifolium pratense L.), winter wheat (Triticum aestivum L.), peas (Pisum sativum L.), potato and barley (Hordeum vulgare L.) followed each other simultaneously on a same field. Data presented in this paper concerned the first 3 years of the rotation during 2009–2011. The experiment was performed with six different farming systems as follows: two organic and four conventional. In both organic farming systems, catch crops (Organic CC) were used to provide organic green manure. In the second organic system, fully composted cattle manure (Organic CC+M) at a rate of 40tha−1 was also added as a fertiliser. The four conventional farming systems differed in the amounts of mineral fertilisers used as follows: N0P0K0 (control), N50P25K95 (low), N100P25K95 (average), or N150P25K95 (high). The average yield as well as tuber N, NO3−and Mg concentrations were significantly influenced by farming systems, year and their interaction. Fresh tuber yields were significantly higher under conventional systems in which nitrogen fertilisers were used. The use of average and high amounts of mineral nitrogen fertilisers increased tuber nitrogen and nitrate concentrations. The use of nitrogen fertilisers slightly decreased tuber Mg concentrations. There were no significant differences among farming systems in average tuber K, Ca, dry matter and starch concentrations. Only the year and its interaction with farming systems had a significant influence on these indicators. Different farming systems had different effects on some soil quality parameters. The Organic CC system significantly decreased the average soil K concentration after potato cultivation. The other organic system, Organic CC+M, significantly increased the average soil Corg and P concentrations after potato cultivation. The conventional control system significantly decreased the average soil Ntot, K and Mg concentrations and increased the P concentration. The conventional system that received 50kgNha−1 significantly decreased the average soil Ntot concentration after potato cultivation. The farming system that received an average amount of mineral nitrogen fertilisers significantly increased the average soil Corg and P concentrations and decreased the soil pH and K after potato cultivation. The conventional system that received 150kgNha−1 significantly decreased the average soil Corg, K and Mg concentrations. The average plant available Ca concentrations before and after potato crops did not have statistically significant differences among systems.