Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy was combined with multivariate data analysis to investigate the chemical changes in wood during particle- and medium density fibreboard (MDF) production of grand fir (Abies grandis [Douglas ex D. Don] Lindl.) and European beech (Fagus sylvatica L.). The mechanical and technological properties of the novel particle- and fibreboards from beech or grand fir wood were similar to those of conventional panels from pine and spruce. This indicates that these timbers can be used as resources for wood-based panel production. Principal component analysis of FTIR spectra differentiated wood, fibres, particles, MDF, and particleboards of both species in the whole production process. Modifications in the spectra of fibres and particles suggested that cellulose properties of wood were changed during mechanical pulping. Different binders and hydrophobic additives were clearly traceable and discernable in wood composites. Samples from the same production step were clustered together, indicating high homogeneity of the raw materials, and intermediate and final products, respectively. This suggests that FTIR spectroscopy in combination with cluster analysis is a useful tool to assess product quality and can be further developed to control and optimize production processes for innovative wood-based panels.