The Notch pathway is a signaling network essential for proper organ development in an embryo, and is indispensable for tissue regeneration in the adult. This key regulatory signaling network is evolutionarily conserved in all metazoans and is continually utilized for the building, maintenance and repair of diverse organs and tissues. Importantly, dysfunctions in the Notch pathway have been demonstrated to result in oncogenic transformation, such as in lymphoid cancers, and have been linked to the pathogenesis of several inherited human diseases. Therefore, the ability to regulate Notch signaling intensity both positively and negatively has a very high therapeutic relevance. Adapting this pathway for tissue engineering applications has great potential to spear-head the development of smart biomaterials to deliberately control cell-fate decisions and lead to designer ex vivo morphogenesis. This review describes the components of Notch-specific signal transduction, presents the role of the Notch signaling network in constructing and repairing multiple organ systems, summarizes the Notch-related pathologies, outlines current advances in the deliberate modulation of the Notch pathway in bioengineering applications, and introduces future perspectives on the use of Notch pathway manipulations as a powerful universal tool in tissue engineering and in the orchestration of stem cell responses. This review also summarizes the existing bioengineering methods most suitable for the deliberate manipulation of Notch signaling, such as smart biomaterials able to pattern Notch ligands or to create gradients of Notch agonists and antagonists. Such methods will likely facilitate the engineering and dynamic remodeling of tissues composed of stem, progenitor and differentiated cells derived from an initially equivalent cell population.