This study aimed to evaluate the influence of pH changes on morphometric parameters of casein micelles and a general overview of their conformational structure through microscopy techniques, Raman spectroscopy and multivariate analysis. It was found that casein micelles morphology and protein secondary structure depend strongly upon pH. The changes of arithmetic average roughness (Ra), size, and shape of casein micelles at different pH are properly characterized by atomic force and cryo-transmission electron microscopy. Morphometric changes of casein micelles were correlated correctly with folding and unfolding of casein molecules as evaluated by Raman spectroscopy when the pH was varied. The novelty of this contribution consists in demonstrating that there is a close structure-functionality relationship between the morphometric parameters of proteins and their secondary structure. Knowledge about casein micelles can help improve their use of its diverse applications.