Utilizing bio-based elements as cement additives has a significant impact on the production of extremely durable and sustainable concrete composites. In the present research work, the effect of a bio-enzyme (Terrazyme) on the strength, durability, and microstructure of RPC was researched at various proportions of Terrazyme (TZ) as binder replacement (0, 0.5, 1, 1.5, 2, and 2.5%). The migration of water and transport properties of concrete are accessed through measurement of the water absorption and gas permeability. Results show that the use of TZ in RPC slightly reduced the compressive strength, and the reduction was more significant at high replacement levels when subjected to water curing. A significant reduction in the permeability of RPC with a relatively low permeability coefficient is obtained even at higher dosages of TZ in autoclaved RPC specimens with greater mechanical strength. In addition, greater chloride penetration with the prolongation of ages is obtained. The inclusion of TZ can not only enhance the waterproofing and penetration resistance of RPC but also achieve economic and ecological benefits.