The effect of Quillaja saponaria saponin, a plant-derived biosurfactant, as an antimicrobial soaking agent in leather manufacturing was investigated in terms of microbial load, total protein content and chemical oxygen demand of residual floats. The antimicrobial activities of three different commercially available saponins (Saponin A, R and S) were tested by using different concentrations of sapogenin (0.125-1g) in soaking process. The concentration of 0.125g Saponin S and 0.25g Saponin R showed the highest similarity to Biocide 1 and 2 for 8h of soaking process respectively. Comparable results to synthetic biocides were obtained from 1g sapogenin treatments of Saponin A and R applications after 24h of soaking process. The total protein content of soaking liquor was increased at higher sapogenin contents in spite of decreased microbial growth which was a well indication of antimicrobial soaking character of saponins. The results showed that Quillaja saponins have the potential to be cheaper, safer and environmentally friendly alternatives to synthetic antimicrobial compounds for leather industry.