Active thylakoids were encapsulated into a three-dimensional silica network to design a photosynthetic bioreactor suitable for harvesting light and splitting water to oxygen. Since these photosynthetic structures are very sensitive to ionic strength and osmotic pressure as well as traces of alcohols, a biocompatible synthesis pathway has been designed to allow the formation of a robust hybrid silica gel without releasing any by-product during its construction. In these conditions, the photochemical activity of thylakoids can be preserved for more than 40 days. This method has successfully been applied to encapsulate more voluminous organelles such as chloroplasts. The present work can be considered as a step forward and comprehensive advance in the field of encapsulation of biological materials from plant systems. © 2009 The Royal Society of Chemistry.