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The aim of the present paper is to evaluate the changes of organic matter during the composting process of fresh winery and distillery residues (WDR) by means of classical and chemometric analysis of (13)C cross-polarization magic angle spinning (CPMAS) NMR and Fourier transform infrared (FT-IR) spectra. (13)C NMR spectroscopy displayed a preferential biodegradation of carbohydrates as well as an accumulation of aliphatic chains (cutin- and suberin-like substances). This preferential biodegradation of the organic fractions reduces the landfill emission potential. Although the composition of the input mixture strongly affects the shape of the infrared (IR) spectra, typical bands of components can be selected and used to follow the composting process; that is, changes in the relative absorbances of the band of nitrate (at 1384 cm(-1)) and in the band of carbohydrates (at 1037 cm(-1)) have been observed. In addition, different chemometric tools, such as partial least-squares (PLS), interval PLS (iPLS), backward iPLS (biPLS), and genetic algorithm (GA), have been used to find the most relevant spectral region during the composting process. Chemometric analysis based on the combined and sequential use of iPLS and GA has been revealed as a very powerful tool for the detection in samples of the most relevant spectral region related to the composting process. From the obtained results, it can be concluded that CPMAS (13)C NMR supported by FT-IR could provide information about the evolution and characteristics of the organic matter during the composting process in order to avoid contamination problems after its use as amendment in agriculture or after landfilling.