<p>This study addresses the microarthropod-based estimation of biological soil quality in rural home gardens using the Qualitative Biological Soil—arthropods (QBS-ar) index. Soil microarthropods, soil properties, soil nutrients, and trace elements were systematically estimated from soil samples collected from 25 home gardens during summer and northeast monsoon seasons over 5 years (2014–2018). The relationships among QBS-ar, microarthropod abundance, soil properties, and soil nutrients were assessed. The microarthropods reported from the study area included Protura, Collembola, Coleoptera, Hymenoptera, Diplopoda, Araneae, Acari, Diptera, and Hemiptera showing statistically significant variations in Summer and monsoon abundance from 2014 to 2018. The QBS-ar index values ranging from 25.28 ± 9.77 to 48 ± 13.12 in summer and from 29.48 ± 18.63 to 56.12 ± 12.55 in monsoon indicated that the home gardens were ranked medium to good in soil quality, with index values ranging from 2 to 4 throughout the study period. Discriminant analysis of soil nutrients with soil properties and microarthropod abundance showed that the 2018 dataset was distinctly separated from the other years. A notable finding was the absence of trace elements (Pb, Cd, Cr) above permissible limits. Hazard estimation through Geographic Information System (GIS), integrating soil properties, nutrients and QBS-ar, indicated that the home gardens functioned as ecosystems with reduced biological soil quality post-flood. This study is among the first to utilize combined QBS-ar scores, soil properties, soil nutrients, and trace elements for long-term soil quality estimation in rural home garden agroecosystems. The study provides a simple, scalable methodological approach for soil ecosystem monitoring and management.</p> Graphical abstract <p></p>