Encapsulation of bioactive substances for extended shelf life and controlled, targeted release is critical for their applications in food and drug delivery. Here, a new method has been developed to encapsulate bioactive molecules in the crystal composites, showing greatly enhanced stability and unique pH-triggered response. Chlorophyll, a model bioactive, is first loaded in shellac nanoparticles via co-precipitation with a high encapsulation efficiency, and then the chlorophyll-loaded nanoparticles are incorporated into calcite crystals grown from a gel media containing the nanoparticles. Under the protection of shellac nanoparticles and calcite crystals, chlorophyll shows excellent stability even under light. Encapsulated chlorophyll could only be released by first dissolving the calcite crystals under acidic condition and then dissolving the shellac nanoparticles under alkaline condition. The unique pH-triggered release mimics the pH change from acidic in the stomach to alkaline in the intestine and is thus well suited for controlled, targeted intestinal release. This work suggests that the crystal composites are an ideal delivery vehicle for the functional design of bioactive molecules.