The presence of methoxypyrazines in Cabernet Sauvignon wines produced from grapes grown in high-altitude and cold-climate regions is common and often treated as regional typicity. These compounds are considered a primary source of herbaceous and vegetal sensory characteristics, which may lead to unpleasant aromas when concentrations exceed the sensory threshold of these substances. Some strategies in the field and during winemaking have been studied with the aim of reducing the content of 2-methoxypyrazines. However, none describe the influence of spontaneous fermentation on the concentration of 2-methoxypyrazines. In this study, EMP (2-ethyl-5(6)-methoxypyrazine), IPMP (2-isopropyl-3-methoxypyrazine), SBMP (2-sec-butyl-3-methoxy-pyrazine), and IBMP (2-isobutyl-3-methoxy-pyrazine) were quantified in Cabernet Sauvignon wines produced via spontaneous fermentation and through fermentation with commercial yeasts. Grapes from vineyards located in the municipalities of Campo Belo do Sul (CBS) and São Joaquim (SJ), both in the state of Santa Catarina, Brazil, were used. Solid phase microextraction (SPME) coupled with the GCMS technique was used for the determination of the compounds. The primary methoxypyrazine found for both production sites was SBMP, with concentrations of 289.26 (CBS) and 681.55 (SJ) ng/L for spontaneous fermentation, and 619.58 (CBS) and 790.62 (SJ) ng/L for commercial yeast fermentation. Additionally, differences were found in other physicochemical quality analyses such as volatile acidity, anthocyanins, and total phenolics. The results indicate that spontaneous fermentation may be used as a strategy to reduce the content of methoxypyrazines in relation to what is present in the grape, particularly when harvest conditions do not allow for complete grape ripening.