During the pretreatment step of ethanol production from renewable resources, formation of the inhibitors can adversly affect the production yields and the environment. The aim of this study was to determine 5-hydroxymethylfurfural (HMF) concentration tolerance of immobilized Saccharomyces cerevisiae during ethanol production in glucose based media and to model ethanol formation, biomass growth, and substrate consumption. Results showed that the highest ethanol yield was calculated as 43.867% (32.07 g/L) in 6 g/L of HMF production. Additionally, the lowest yield and production values were obtained as 32.14% and 3.993 g/L when the system was run with 10 g/L of HMF. Compared to biomass growth, sugar consumption and ethanol production were less affected by HMF. Furthermore, according to modeling parameters (BF, AF, RMSE MAE, and R2 values), Baranyi successfully represented ethanol production, whereas Weibull was chosen as the best model for the representation of sugar consumption and biomass production.