Andean crops like quinoa, amaranth, maize, kañiwa, and local legumes are known for being more nutritious than many conventional grains. They also contain natural compounds that support health, making them excellent ingredients for functional foods. These grains are especially rich in starch and protein, which give them unique properties that are attracting growing interest in the food industry. The chapter takes a closer look at how traditional and modern processing methods are being used to enhance the functionality of key Andean grains—most notably quinoa and amaranth. These pseudocereals have drawn growing interest for their nutritional value and their potential in sustainable food systems. Techniques such as extrusion, alkaline extrusion, nixtamalization, roasting, germination, enzymatic hydrolysis, and fermentation, which could potentially alter the structural properties of starches and proteins, are discussed in detail. Special attention is given to the use of biophysical tools—like X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, and confocal laser scanning microscopy (CLSM)—to understand the molecular changes occurring during these processes. These techniques offer valuable insights, either on their own or in combination with chemical analyses, helping researchers decode how starches, proteins, and other macronutrients behave and interact.