The encapsulation of living plant cells into materials could offer the possibility to develop new green biochemical technologies. With the view to designing new functional materials, the physiological activity and cellular response of entrapped cells within different silica-based matrices have been assessed. A fine-tuning of the surface chemistry of the matrix has been achieved by the in situ copolymerization of an aqueous silica precursor and a biocompatible trifunctional silane bearing covalently bound neutral sugars. This method allows a facile control of chemical and physical interactions between the entrapped plant cells and the scaffold. The results show that the cell-matrix interaction has to be carefully controlled in order to avoid the mineralization of the cell wall which typically reduces the bioavailability of nutrients. Under appropriate conditions, the introduction of a trifunctional silane (ca. 10%) during the preparation of hybrid gels has shown to prolong the biological activity as well as the cellular viability of plant cells. The relations of cell behavior with some other key factors such as the porosity and the contraction of the matrix are also discussed.