A method of modifying a virtual application configuration to include modifications made at runtime by a virtual application that is implemented by a first virtualized application file that was created previously using the virtual application configuration. At runtime, the virtual application implemented by the first virtualized application file stores modifications to its configuration in a sandbox memory location. The method includes reading the modifications from the sandbox memory location. Then, the modifications are written to the virtual application configuration. The modified virtual application configuration is then used to create a second virtualized application file that includes the modifications stored in the sandbox memory location.