The use of bio-based material for repairing concrete is a relatively new method. Therefore, more results from simulated real-condition experiments are needed before being applied on a practical scale. In the recent past, several studies have been conducted on the improvement of bio-based repair materials. In this study, the bio-based material involving yeast, glucose, and calcium acetate mixed in a Tris buffer solution showed the potential to develop a microbial process leading to the precipitation of calcium carbonate. We investigated the factors affecting the precipitation rate of the calcium carbonate of bio-based materials for repairing leakage in the concrete specimens. Based on a series of experiments involving temperature, the type of dry yeast, and the concentration of the Tris buffer solution, the composition of bio-based materials with the highest precipitation rate of calcium carbonate was selected. The selected mixture could be applied to repair leakage of concrete until the cracks are sealed entirely.