Characterization and quantification of individual whey proteins are of crucial importance to many industrial dairy processes. Labor intensive wet-chemical methods are still being used for this purpose, but a rapid quantification method for individual whey proteins is highly desired. This work investigate the utility of Fourier transform mid-infrared spectroscopy and Fourier transform near-infrared spectroscopy for rapid quantification of the two main whey proteins (β-lactoglobulin and α-lactalbumin) in complex aqueous whey solutions simulating production process streams. MIR and NIR spectra obtained on whey samples with known and varying amounts of the proteins of interest and are used to develop partial least squares prediction models. Selection of informative wavelength regions allowed for prediction of β-lactoglobulin and α-lactalbumin concentrations with very high precision and accuracy (root mean square error of cross-validation, or RMSECV, of 0.6% and R² of 0.99 for NIR), demonstrating the potential of being implemented for rapid in-line monitoring of protein composition in industrial whey streams. Two-dimensional MIR-NIR correlation spectroscopy is used to identify the most informative parts of the NIR spectra in relation to protein secondary structure. In addition multivariate curve resolution is applied to the MIR data to resolve mixture spectra and to elucidate the spectral ranges that were most useful in distinguishing between the two whey proteins. The study concludes that NIR spectroscopy has potential for accurate in-line protein quantification and overall secondary protein structure quantification which open new possibilities for in-line industrial applications.