Pectin is a biocompatible polysaccharide with intrinsic biological activity, which may exhibit different structures depending on its source or extraction method. The extraction of pectin from various industrial by-products presents itself as a green option for the valorization of agro-industrial residues by producing a high commercial value product. Pectin is susceptible to physical, chemical, and/or enzymatic changes. The numerous functional groups present in its structure can stimulate different functionalities, and certain modifications can enable pectin for countless applications in food, agriculture, drugs, and biomedicine. It is currently a trend to use pectin to produce edible coating to protect foodstuff, antimicrobial bio-based films, nanoparticles, healing agents, and cancer treatment. Advances in methodology, use of different sources of extraction, and knowledge about structural modification have significantly expanded the properties, yields, and applications of this polysaccharide. Recently, structurally modified pectin has shown better functional properties and bioactivities than the native one. In addition, pectin can be used in conjunction with a wide variety of biopolymers with differentiated properties and specific functionalities. In this context, this review presents the structural characteristics and properties of pectin and information on the modification of this polysaccharide, its respective applications, perspectives, and future challenges.