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Commercially available homogenized cow- and plant-based milks were investigated by optical spectroscopy in the range of 400–1360 nm. Absorbance spectra, the effective scattering coefficient μs′, and the spectral absorption coefficient μa were recorded for 23 milk varieties and analyzed by multivariate data analysis. Cow- and plant-based milks were compared and discriminated using principal component analysis combined with a quadratic discriminant analysis. Furthermore, it was possible to discriminate the origin of plant-based milk by μa and the fat content in cow-based milk by μs′. Partial least squares regression models were developed to determine the fat content in cow-based milk. The model for μs′ proved to be the most efficient for this task with R2 = 0.98 and RMSEP = 0.19 g/100 mL for the external validation. Thus, optical spectroscopy together with multivariate data analysis is suitable for routine laboratory analysis or quality monitoring in the dairy production.