Scanning electron microscopy (SEM) is a robust technique to characterize the micro and nanostructure of starches and flours. This chapter presents a practical, step-by-step protocol, from specimen preparation to image capture and interpretation, to assess native granule morphology and processing-induced changes. Samples (powders or tissue fragments) are sectioned, dried below the starch gelatinization temperature (≈40–45°C) or lyophilized, stored over desiccant, mounted on carbon tape stubs, and sputter-coated with gold or carbon to improve surface conductivity. Imaging is carried out under low vacuum with progressive magnifications (e.g., 100× to >5000×), using secondary electrons for topographic contrast and backscattered electrons for atomic-number contrast; optional EDS can complement surface analysis. The protocol details focusing, lens alignment, and recording parameters, and highlights common artifacts (charging and residual moisture) and their prevention. Representative micrographs illustrate how SEM reveals granule size, shape, distribution, surface features, and growth rings, which are influenced by botanical origin and amylose/amylopectin ratio. The workflow also supports monitoring enzymatic, chemical, and physical modifications. Together, these procedures provide reliable, high-resolution images, and practical guidance for consistent morphological evaluation of starch and flour systems.