The objective of this research focuses on the development of a statistical methodology able to answer the question of whether variation in the intake of sulfur amino acids (SAA) affects the metabolic process. Traditional approaches, which evaluate specific biomarkers after a series of preprocessing procedures, have been criticized as not being fully informative, as well as inappropriate for translation of methodology. Rather than focusing on particular biomarkers, our proposed methodology involves the multifractal analysis that measures the inhomogeneity of regularity of the proton nuclear magnetic resonance (1H-NMR) spectrum by wavelet-based multifractal spectrum. With two different statistical models (Model-IandModel-II), three different geometric features of the multifractal spectrum of each1H-NMR spectrum (spectral mode, left slope, and broadness) are employed to evaluate the effect of SAA and discriminate1H-NMR spectra associated with different treatments. The investigated effects of SAA include group effect (high and low doses of SAA), depletion/repletion effect, and time over data effect. The1H-NMR spectra analysis outcomes show that group effect is significant for both models. The hourly variation in time and depletion/repletion effects does not show noticeable differences for the three features inModel-I. However, these two effects are significant for the spectral mode feature inModel-II. The1H-NMR spectra of the SAA low groups exhibit highly regular patterns with more variability than that of the SAA high groups for both models. Moreover, the discriminatory analysis conducted using the support vector machine and the principal components analysis shows that the1H-NMR spectra of SAA high and low groups can be easily discriminatory for both models, while the spectra of depletion and repletion within these groups are discriminatory forModel-IandModel-II. Therefore, the study outcomes imply that the amount of SAA is important and that SAA intake affects mostly the hourly variation of the metabolic process and the difference between depletion and repletion each day. In conclusion, the proposed multifractal analysis of1H-NMR spectra provides a novel tool to investigate metabolic processes.