Not only enjoyed as delicacy, soups of vegetables, fish or meat are also served as folk remedies in many cultures. The formation of nanostructures was observed both in the hepato-protective freshwater clam soup and the anti-diabetic bitter melon soup. It was in accompany with either the migration of clam compositions into the soup or the progression of Maillard reaction in bitter melon. The biochemical compositions, bioactivities and colloidal characteristics of those nano-particles were preliminarily investigated. It implies that the nanostructures may probably be the functioning unit, and provide a novel perspective to understanding the complicated food system.