Alongside the increasing proofs of efficacy of miniaturized NIR instruments in food-related scenarios, it is progressively growing the number of end-users, even incentivized by the low-cost of the sensors. While attention is paid to the analytical protocol–from sampling to data collection, up to the data processing, the importance of error investigation in raw data is generally underestimated. Understanding the sources and the structure of uncertainty related to the raw data improves the quality of measurements and suggests the correct planning of the experiments, as well as helps in chemometric model development. The goal of chemometric modeling is to separate information from noise; therefore, a description of the nature of measurement error structure is necessary. Among the different approaches, we present the study of the Error Covariance Matrices (ECMs) and their decomposition in a bilinear structure as a powerful method to study the main sources of variability when using miniaturized NIR sensors in the actual way of use. Granulated and lump sugar samples were chosen as the case study and analyzed with two miniaturized spectrometers working in the NIR regions around 1350–2550 nm and 900–1750 nm, respectively, in dispersive reflectance mode. Results show that having some insights on multivariate measurement errors associated with spectra could be interesting in paving the way for several applications.