Mouldboard ploughing has been associated with a loss in soil quality, while reduced tillage is often reported to result in crop yield declines. Occasional ploughing every few years could be an attractive compromise, but it remains unclear whether such a system results in a combined benefit of improved crop yield and soil quality. Here, we present data from a 43-year old field experiment on a clay soil in central Sweden. We analysed how three different tillage systems – annual mouldboard ploughing, continuous shallow tillage, and shallow tillage with occasional mouldboard ploughing – affect crop yields and soil properties with the objective of assessing joint response patterns between crop production and soil quality indicators reflecting soil structure, soil organic carbon storage, and habitat for soil biota. Crop yields were not affected by the tillage systems. Characteristics of the soil pore system and soil biota were similar in the occasional ploughing and annually mouldboard ploughed systems. Shallow tillage significantly altered microbial community composition relative to ploughed treatments, increasing bacterial and fungal abundances and reducing diversity in the upper topsoil layer, likely due to stratified soil carbon stocks. There was also a higher proportion of biopores in shallow tillage, which could be advantageous during dry spells that are expected to become more frequent and severe with climate change. Nevertheless, there were only small effects on water retention, biomass of nematodes and earthworms, and most of the abiotic soil properties. We conclude that occasional ploughing did not offer advantages at our site, and our results show that no system improved yield and all soil quality indicators simultaneously