This study employed native soil bacteria to modify the soil properties with an aim to use biomodification for engineering soil behaviour. It was found that the biomodification impacted the soil behaviour to varying degrees under different conditions. Various aspects that have been considered in the assessment are the shear strength, flow behaviour, water retention and thermal properties of the soils. While of these properties varied significantly with biomodification, a few of them have shown little or no significant changes. Also, in order to simulate the soil-water interactions, this study developed a novel analytical framework based on mixture coupling theory to model water retention and drying processes in soils. Further, through this study, field trials were conducted to assess the impact of organic and synthetic nitrogen sources on the crop quality and soil microbiome diversity. The organic source of nitrogen proved to enhance protein content in wheat. The addition of synthetic nitrogen impacts the microbiome quality of agricultural soils. This is seen in the fungal diversity and relative enrichment of key bacteria associated with the nitrogen cycle.