The eSciDoc system supports various metadata schemata or profiles. In fact, the basic services (e.g., Item Handler and Container Handler) take a metadata-agnostic approach. They accept every well-formed XML tree as metadata record. Additionally, each Container and Item may have more than just one metadata record.

On the solution layer however, the metadata schema is typically well-defined and specific to the application context. For the first eSciDoc solutions, a eSciDoc-specific metadata schema has been developed.