The flour milling industry, a vital component of global food production, is undergoing a transformative phase driven by the integration of smart devices and advanced technologies. This transition promises improved efficiency, quality, and sustainability in flour production. Accurate estimation of protein, moisture and ash content in wheat grains and flour is of paramount importance due to their direct impact on product quality and compliance with industry standards. This paper explores the application of Near-Infrared (NIR) spectroscopy as a non-destructive, efficient, and cost-effective method for measuring the aforementioned essential parameters in wheat and flour, by investigating the effectiveness of a low-cost handle NIR spectrometer. Furthermore, a novel approach using Fuzzy Cognitive Maps (FCMs) is proposed to estimate protein, moisture and ash content in grain seeds and flour, marking the first known application of FCMs in this context. Our study includes an experimental setup that assesses different types of wheat seeds and flour samples and evaluates three NIR pre-processing techniques to enhance parameter estimation accuracy. The results indicate that low-cost NIR equipment can contribute to the estimation of the under-study parameters.