Stabilisation of soil has been carried out by many researchers in the past using conventional materials such as lime, fly-ash, silica fumes, quarry dust and so on. Ground improvement using enzymes or micro-organisms, fermented from vegetable extracts, has been one of the latest sustainable invents in geotechnical engineering. This study explores and compares the effectiveness of terrazyme in improving the mechanical properties such as strength and compressibility characteristics of locally available soils. The experimental studies are extended to two soils that possess extreme characteristics namely lateritic and black cotton (BC). The study is carried out on three different dosages of terrazyme, namely 150, 200 and 250 ml/m3, respectively, obtained through volumetric proportioning. To understand the long-term behaviour pattern of terrazyme, studies are carried out on varying curing periods (7 and 28 days) and the results are compared. The results highlight that terrazyme modification is more effective in BC soil than lateritic soil. To evaluate the changes in soil fabric brought about on the account of application of enzyme, scanning electron microscopy and energy-dispersive analysis of X-ray studies are carried out. The design of flexible pavements with an enzyme-modified subgrade revealed a more robust and sustainable infrastructure solution.