<p>The incorporation of bio-enzymes into pavement stabilization has emerged as a sustainable alternative to conventional chemical stabilizers, offering improved strength and durability. This study investigates the effect of Cement, Terrazyme, a commercially available bio-enzyme, and their combination on different Soil-Aggregate Mixes (SAMs). The SAMs were collected from other parts of India across 40 road sections and sub-grouped into five different SAMs based on their Plasticity Index (PI) value. Laboratory investigations were conducted on SAMs stabilized with an optimum cement dosage, both with and without bio-enzyme, to evaluate their strength and durability characteristics. Tests, including Unconfined Compressive Strength (UCS), flexural strength, and Resilient Modulus (M_R), were conducted to determine the mechanical behavior. Durability characteristics were evaluated using wetting–drying cycles. The microstructural analysis of treated Mixes was also done using a Scanning Electron Microscope (SEM). The results indicated that bio-enzyme inclusion enhanced early-age strength gain, improved flexural performance, and improved moisture resistance compared to conventional cement-treated mixes. Enzymatically treated mixes show improvements in MDD, a reduction in OMC by 7.30–9.11%, an increase in UCS value from 7 to 28 days of 29.25–71.09%, a decrease in durability mass loss percentage by 4.41–8.08%, an improvement in residual UCS, and significant improvements in MR values. The subject of this study is a modern and important one, as it involves the use of bio-enzymes as a sustainable alternative to cement in soil stabilization, a field of great importance in road engineering and sustainability.</p>