Alcoholic fermentation is a key step in wine production. Indeed, a wide range of compounds, which strongly affect the sensory properties of wine, is produced during this process. While Saccharomyces cerevisiae yeast cultures are commonly employed in winemaking to carry on the fermentation process, some non-Saccharomyces species have recently gained attention due to their ability to produce various metabolites of oenological interest. The use of different yeasts strains usually results in wines with different sensory properties, despite being obtained from the same grape variety. In this paper, we tested the feasibility of using near-infrared spectroscopy (NIR) to discriminate among red wines from three different grape varieties produced with pure S. cerevisiae or by mixed fermentation with a promising non-Saccharomyces yeast, namely the Starmeriella bacillaris, which usually yields wines with significant amounts of glycerol and low levels of ethanol, acetic acid, and acetaldehyde. A principal component analysis (PCA) performed on the NIR spectra was used to search for differences in the samples. The NIR results have been compared with both basic wine parameters and sensory analysis data.