A method to maintain residual enzyme activity for prolonged time in harsh aqueous media such as high pH and organic solvents is presented. As an example, horseradish peroxidase (HRP) was encapsulated into a silica matrix using the nonsurfactant templated method for producing sol-gel mesoporous materials that has been invented by our group. Fructose was used as the nonsurfactant template. The porous silica containing the enzyme was then coated with a mixture of acrylic monomer (triethyleneglycol dimethacrylate) and polyethylene glycol (PEG) followed by photopolymerization and crushed to get the doubly encapsulated enzyme powder. This double encapsulation ensures that the enzyme remains active and that it is not in direct contact with the harsh media. The activity of the encapsulated HRP was tested after being submerged in ethanol, laundry detergent and buffer solution of pH=10 for 24 hours and the data were compared to those of native unprotected HRP under the same conditions. Results indicate the doubly encapsulated enzyme shows much higher activity compared to the native enzyme. Our studies suggest that this new double encapsulation system could maintain the activity of various enzymes and other biomacromolecules, while they are stored and/or used in harsh environments, and may have potential applications in health care, medicine, biosensors and biocatalysis.