Screening of chemical, biochemical and biomolecule-nanoparticle methods for the inhibition of Candida krusei were evaluated without hampering the growth of dairy yeast Kluyveromyces marxianus. The effective inhibition was observed with the help of H2O2, Williopsis saturnus, at specific combination of pH and temperature (pH 5.0 and 40 °C) and Ag-KT4561 nanoparticles among the various methods used. However, the most efficient inhibition was observed with Ag-KT4561 nanoparticles. In general H2O2 works best at pH range 4.0 to 10.0 and at temperature 30 °C or above. H2O2 concentration of 4000 ppm at 45 °C and pH 5.5 exhibited significant inhibition of C. krusei, while K. marxianus remains unaffected. But, when used with lyophilized supernatant of W. saturnus, 2400 ppm H2O2 was effective. Further, nanoparticle with silver was synthesized to reduce the quantity of killer protein and enhance the efficiency of protein. Complete inhibition of C. krusei was observed at 350 µM of synthesized silver nano-particle (AgNPs) of the killer protein from W. saturnus, with little effect on K. marxianus concentration. A stability test confirms the effect of protein silver nanoparticles on C. krusei for more than 20 weeks without any change in pH and temperature. Thus, the nanoparticles could be potentially used for inhibition of C. krusei without affecting the growth of K. marxianus and the process could be run non-aseptically.