Agricultural intensification is one of the greatest threats to soil biota and function. In contrast, set-aside still remains a management practice in certain agri-environmental schemes. In Hungary, the establishment of sown set-aside fields is a requirement of agri-environmental schemes in High Nature Value Areas. We tested the effects of set-aside management on soil biota (bacteria, microarthropods, woodlice and millipedes), soil properties and organic matter decomposition after an initial establishment period of two years. Cereal – set-aside field pairs, semi-natural grasslands and cereal fields were sampled in the Heves Plain High Nature Value Area in Eastern Hungary, in May 2014. Topsoil samples were taken from each site for physical, chemical, microbial analyses and for extraction of soil microarthropods. Macrodecomposers were sampled by pitfall traps for two weeks. The biological quality of soil was estimated by the integrated QBS index (‘‘Qualità Biologica del Suolo’’, meaning ‘‘Biological Quality of Soil’’) based on diversity of soil microarthropods. To follow early stage organic matter decomposition, we used tea bags filled with a site-independent, universal plant material (Aspalathus linearis, average mass 1.26 ± 0.03 g). Tea bags were retrieved after 1 month to estimate the rate of mass loss. We found significant differences between habitat types regarding several soil physical and chemical parameters (soil pH, K and Na content). The study showed positive effects of set-aside management on soil biodiversity, especially for microarthropods and isopods. However, we did not experience similar trends in relation to soil bacteria and millipedes. There was higher intensity of organic matter decomposition in soils of set-aside fields and semi-natural grasslands (remaining mass on average: 74.17% and 76.6%, respectively) compared to cereal fields (average remaining mass: 81.3%). Out of the biotic components, only the biological quality of soil significantly influenced (even if marginally) plant tissue decomposition. Our results highlight the importance of set-aside fields as shelter habitats for soil biota, especially for arthropods. Set-aside fields that are out of a crop rotation for 2 years could be a valuable option for maintaining soil biodiversity, as these fields may simultaneously conserve elements of above- and below-ground diversity.