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Emerging portable near infrared (NIR) spectroscopic approaches coupled with data analysis and chemometric techniques provide opportunities for the rapid characterization of spray-dried products and process optimization. This study aimed to enhance the understanding of applying NIR spectroscopy in spray-dried samples by comparing two sample preparation strategies and two spectrometers. Two sets of whey protein–maltodextrin matrixes, one with a protein content gradient and one with a consistent protein content, were spray-dried, and the effect of the two preparation strategies on NIR calibration model development was studied. Secondly, a portable NIR spectrometer (PEAK) was compared with a benchtop NIR spectrometer (CARY) for the moisture analysis of prepared samples. When validating models with the samples with focused protein contents, the best PLS protein models established from the two sample sets had similar performances. When comparing two spectrometers, although CARY outperformed PEAK, PEAK still demonstrated reliable performance for moisture analysis, indicating that it is capable as an inline sensor.