Breast milk is an optimal food that covers all the nutritional needs of the newborn. It is a dynamic fluid whose composition varies with lactation period. The neonatal units of hospitals have human milk banks, a service that analyzes, stores, and distributes donated human milk. This milk is used to feed premature infants (born before 32 weeks of gestation or weighing less than 1500 g) whose mothers, for some reason, cannot feed them with their own milk. Here, we aimed to develop near-infrared spectroscopy (NIRS) measures for the analysis of breast milk. For this purpose, we used a portable NIRS instrument scanning in the range of 1396–2396 nm to collect the spectra of milk samples. Then, different chemometrics were calculated to develop 18 calibration models with and without using derivatives and the standard normal variate. Once the calibration models were developed, the best treatments were selected according to the correlation coefficients (r2) and prediction errors (SECVs). The best results for the assayed macronutrients were obtained when no pre-treatment was applied to the NIR spectra of fat (r2 = 0.841, SECV = 0.51), raw protein (r2 = 0.512, SECV = 0.21), and carbohydrates (r2 = 0.741, SECV = 1.35). SNV plus the first derivative was applied to obtain satisfactory results for energy (r2 = 0.830, SECV = 9.60) quantification. The interpretation of the obtained results showed the richness of the NIRS spectra; moreover, the presence of specific bands for fat provided excellent statistics in quantitative models. These results demonstrated the ability of portable NIRS sensors in a methodology developed for the quality control of macronutrients in breast milk.