Soil health is a key priority for assessing environmental safety and achieving the European Union’s climate and biodiversity targets. Changes in edaphic diversity are the first indicators of soil health, but require long-term monitoring. Therefore, integrated approaches with minimal ecological and economic impact are essential. This study explores the potential of behavioural bioassays, specifically avoidance and disaggregation responses, as rapid indicators of soil habitat degradation, following the principle of limited habitat functions. Given the metrics of biodiversity loss and behavioural responses analysis are not aligned, a multi-approach comparative study was conducted to link multispecies behavioural responses with in situ measures of soil biodiversity. Behavioural tests using model organisms were employed to detect signs of habitat depopulation or fragmentation. These data were then compared with structural and functional diversity metrics of soil invertebrate and microbial communities, summarised using standard ecological indices. The results showed consistent metrics between model organisms’ responses and levels of invertebrate diversity. Specifically, soils that altered population behaviour also showed a reduction in edaphic invertebrate structural and functional diversity. However, these changes did not emerge from microbial analysis, suggesting that metrics linking ecological responses of model organisms to changes in microbial diversity are yet to be investigated. This study suggests that behavioural bioassays, in combination with invertebrate diversity assessments, offer a valuable, early-warning tool for identifying soils at risk. Such integrative methodologies could support more targeted and efficient soil monitoring and restoration efforts, contributing to broader environmental protection and sustainability goals.