Second generation (2G) ethanol is produced using lignocellulosic biomass. However, the pre-treatment processes generate a variety of molecules (furanic compounds, phenolic compounds, and organic acids) that act as inhibitors of microbial metabolism, and thus, reduce the efficiency of the fermentation step in this process. In this context, the present study aimed to investigate the effect of furanic compounds on the physiology of lactic acid bacteria (LAB) strains that are potential contaminants in ethanol production. Homofermentative and heterofermentative strains of laboratory LAB, and isolated from first generation ethanol fermentation, were used. LAB strains were challenged to grow in the presence of furfural and 5-hydroxymethylfurfural (HMF). We determined that the effect of HMF and furfural on the growth rate of LAB is dependent on the metabolic type, and the growth kinetics in the presence of these compounds is enhanced for heterofermentative LAB, whereas they are inhibitory to homofermentative LAB. Sugar consumption and product formation were also enhanced in the presence of furanic compounds for heterofermentative LAB, who displayed effective depletion kinetics when compared to the homofermentative LAB. Homo- and heterofermentative LAB are affected differently by furanic compounds, in a way that the latter type is more resistant to the toxic effects of these inhibitors. This knowledge is important to understand the potential effects of bacterial contamination in 2G bioprocesses.