The high sensitivity Compton and Rayleigh X-ray scattering signals can be used to gain valuable information on the chemical composition of various matrices, by exploiting the ratio of those signals as a function of the effective atomic number (Zeff). Neither total reflection X-ray fluorescence (TXRF) nor the effect of the experimental setup, including sample preparation, X-ray excitation source selection, and band deconvolution procedure, has been assessed in this kind of approach. Here, a Compton/Rayleigh ratio and Zeff-based TXRF method was set up and tested as an analytical tool for milk samples differentiation. The method was developed using a 90° scattering angle and assessed using different X-ray excitation sources: a molybdenum tube (Mo Kα 17.5 KeV) and a tungsten tube (W Lα 8.5 KeV and W-Brems 35 KeV). The evaluation of independent Compton and Rayleigh signals was performed by non-Gaussian and Gaussian curve resolution methods, and both height and area-based calculations were evaluated. Different sample preparation conditions were assessed. By using 11 standard materials, a calibration curve for Compton/Rayleigh ratio versus Zeff was established. The method was tested to determine the Zeff of milk samples, which enabled its use as a parameter to differentiate them. Good precisions were obtained with the Mo excitation source and the area-based calculations, which allowed to differentiate undiluted milk samples by species, treatment, and fat content according to their Compton/Rayleigh ratio. This simple and rapid method has the potential to be used for the differentiation of various types of samples, including liquids, solids, and aerosols.