Various embodiments of a system and method for enhancing applications for Java Data Object (JDO) persistence are disclosed. A class structure based data object enhancer may operate on the classes of an application in the absence of user input, to produce metadata to determine a persistence structure corresponding to the application classes. The class structure based data object enhancer may use the generated metadata to produce enhanced application classes. For example, the class structure based data object enhancer may incorporate calls to a JDO persistence mechanism into a class at each point where a field designated by the persistence structure to be persisted, is accessed. The class structure based data object enhancer may also generate a database schema, which may specify how the fields designated for persistence are stored in a persistent data store.