Protein adulteration is a common fraud in the food industry due to the high price of protein sources and their limited availability. Total nitrogen determination is the standard analytical technique for quality control, which is incapable of distinguishing between protein nitrogen and nitrogen from non-protein sources. Three benchtops and one handheld near-infrared spectrometer (NIRS) with different signal processing techniques (grating, Fourier transform, and MEM—micro-electro-mechanical system) were compared with detect adulteration in protein powders at low concentration levels. Whey, beef, and pea protein powders were mixed with a different combination and concentration of high nitrogen content compounds—namely melamine, urea, taurine, and glycine—resulting in a total of 819 samples. NIRS, combined with chemometric tools and various spectral preprocessing techniques, was used to predict adulterant concentrations, while the limit of detection (LOD) and limit of quantification (LOQ) were also assessed to further evaluate instrument performance. Out of all devices and measurement methods compared, the most accurate predictive models were built based on the dataset acquired with a grating benchtop spectrophotometer, reaching R2P values of 0.96 and proximating the 0.1% LOD for melamine and urea. Results imply the possibility of using NIRS combined with chemometrics as a generalized quality control tool for protein powders.