The need for reliable biological indicators to support soil biomonitoring is increasing, particularly in agricultural systems where management practices and environmental pressures interact to influence soil ecological integrity. Among soil fauna-based indicators that measure soil health, the Soil Biological Quality indices based on microarthropods (QBS-ar) and earthworms (QBS-e) provide functional measures of soil condition, however their combined application remains largely unexplored. In this study, for the first time both indices were applied simultaneously to assess soil biological quality in the same agroecosystem. The context was that of contrasting agricultural systems (strip cropping vs. pure stands) in a real-farm experimental set-up. Additional biological variables and soil physico-chemical parameters were also considered. Statistical analyses included Spearman correlations, linear mixed-effect models (LMMs), and redundancy analysis (RDA). QBS-ar and QBS-e showed contrasting responses to management systems, with higher QBS-ar values under strip cropping and higher QBS-e values in pure stands. No significant relationship was observed between the two indices. Multivariate analyses indicated that both indices were significantly influenced by management and environmental variables, although with different patterns of association. QBS-ar appeared more responsive to variation in topsoil conditions, whereas QBS-e was associated with broader soil properties and seasonal community dynamics. These results indicate that QBS-ar and QBS-e capture complementary aspects of soil biological quality and should not be used interchangeably. Their combined use improves the interpretation of soil biological responses to agricultural management and associated environmental pressures. Overall, this study highlights the potential of soil fauna-based indices as practical tools for biomonitoring in agroecosystems and supports further exploration on the comparative responses of biological indexes.