This study indicates the significance of biological soil amendment (GS: garlic stalk) and microbial inoculation (AM: Arbuscular mycorrhizal fungi) for improving the degraded soil conditions and micro-ecological sustainability within an efficient resource use framework. Soil quality indicators and the soil micro-environment of vulnerable and degraded soil significantly improved through the consecutive application of organic input and biological soil amendments under the repeated growing regime (2016-2018). The present study explored the dynamical changes in soil structure and micro-environment along with cucumber yield and identified the belowground soil-microbiota mechanism of compatible host plant interaction and positive synergism between organic residue and fungal inoculants within the roots and roots within the soil.