Query objects can be compiled via the compile method. Compiling a query is a hint to the implementation to optimize an execution plan for the query. During compilation, all query elements are validated; any inconsistencies are reported via a JDOUserException.

Query instances can also be serialized. After deserialization, a query cannot be executed, but it retains its candidate class, filter string, imports, parameters, variables, and ordering. A deserialized query can therefore act as a template to create other query instances with the same configuration. This is accomplished through the PersistenceManager's newQuery(Object template) method.