•“Pheophorbidation” reactions were observed for the first time during in vitro digestion of chls.•During in vitro digestion, chls were more oxidized than pheophorbides and pheophytins.•The digestive stability of chl c derivatives were determined for the first time.•Extracellular structure of seaweeds determines the in vitro digestion recovery of chls. The three most common edible seaweeds, Nori (Porphyra umbilicalis), Sea Lettuce (Ulva sp.) and Kombu (Laminaria ochroleuca), were subjected for the first time to an in vitro digestion process in order to study the digestive stability and recovery of chlorophyll pigments of the a, b and c series. Due to the complex and diverse chlorophyll profile in these seaweeds, new principles regarding the behaviour of chlorophylls during the in vitro digestion were obtained. Thus, the in vitro digestion conditions favoured the pheophytinisation reaction of the a series in comparison with the b and c series; oxidation reactions were promoted for chlorophylls instead of pheophorbides and pheophytins; the conversion of pheophytin to pheophorbide was observed for the first time during in vitro digestion and only occurred when the initial chlorophyll profile contained a large proportion of pheophytins. The extracellular matrix of the seaweeds was the main determining factor in the recovery of pigments after in vitro digestion, with significant differences between seaweed species. The novel chlorophyll behaviour observed for digestive, stability and recovery patterns obtained in the present work are applicable to other food matrices.