Wine aging in wooden barrels improves the final products’ sensory profile and increases the price. Among the different types of woods, the International Enological Codex of the International Organisation of Vine and Wine (OIV) approves only the use of Oak and Chestnut, thus producing a need for fast and cost‐effective authentication methods. In this study Fourier Transform (FT)‐mid‐infrared (IR) spectroscopy combined with chemometrics was employed to analyze and discriminate wines aged in barrels made from different type of wood species and in stainless steel tanks, over a period of 12 months. The wines used were made from four indigenous Greek grape varieties, two white and two red. A complete differentiation of the samples was achieved according to grape variety, the container type and the aging time based on two spectral regions (from 1800 to 1500 cm⁻¹ and from 1300 to 900 cm⁻¹) of their FT‐IR spectra.