Hydrogels are proving to be very versatile as wound healing devices. In addition to their capabilities of providing a moist cellular environment and adaptive mechanical properties mimicking the extracellular matrix, they allow the incorporation of small molecules, which have potential impacts on cellular behaviour, in their nanostructures. This strategy can allow for specific targeting of the different stages of wound healing namely hemostasis, inflammation, and proliferative and remodelling phases. The latter include interlinked processes such as angiogenesis, collagen synthesis, growth factor release, collagen maturation and re-epithelialization. In this review, we attempt to match the mechanisms of action of natural molecules/extracts to the different stages of wound healing so that they can be used in a novel approach of multiphase-directed tissue regeneration using loaded hydrogel scaffolds.