Analysis of bovine milk proteins is crucial in many food and non-food industrial applications, nevertheless labour-intensive wet-chemical, low-throughput methods are still routinely used. In this work, external cavity-quantum cascade laser (EC-QCL) mid-infrared spectroscopy is employed as a rapid method for protein analysis of commercial bovine milk. Combined analysis of the amide I and II bands enabled quantitation of individual proteins (casein, β-lactoglobulin, α-lactalbumin) and total protein content. IR spectra of spiked and diluted milk samples were employed for calibration of the target analytes in the presence of a complex matrix by partial least squares (PLS) regression modelling. A sample set of different milk types ( pasteurized; differently processed extended shelf life, ESL; ultra-high temperature, UHT) was analysed, and results agreed well with reference methods. Quantitation of temperature sensitive proteins enables detailed distinction between milk types experiencing different heat loads during processing, and discrimination between diverse bovine milk types is successfully demonstrated.