A microfluidic approach for raw milk sample preconditioning prior to protein and lipid content analysis has been developed. The system utilizes microchip acoustophoresis and is a further extension of our previously reported multiple node ultrasonic standing wave focusing platform (Grenvall, C., Augustsson, P., Matsuoka, H. and Laurell, T. Proc. Micro Total Anal. Syst. 2008, 1, 161-163). The microfluidic approach offers a method for rapid raw milk quality control using Fourier transform infrared spectroscopy (FT-IR). Two acoustophoresis modes are explored, 2 lambda/2 and 3 lambda/2, offering lipid content enrichment or depletion, respectively. Lipid content depletion above 90% was accomplished. FT-IR data on microchip-processed raw milk samples, enabling direct lipid and protein content analysis, are reported. Most importantly, the harmonic operational modes bypass the problem of lipid aggregation and subsequent clogging, inherent in lambda/2 acoustophoresis systems.