Systems and methods for single instance storage operations are provided. Systems constructed in accordance with the principals of the present invention may process data containing a payload and associated metadata. Often, chunks of data are copied to traditional archive storage wherein some or all of the chunk, including the payload and associated metadata are copied to the physical archive storage medium. In some embodiments, chunks of data are designated for storage in single instance storage devices. The system may remove the encapsulation from the chunk and may copy the chunk payload to a single instance storage device. The single instance storage device may return a signature or other identifier for items copied from the chunk payload. The metadata associated with the chunk may be maintained in separate storage and may track the association between the logical identifiers and the signatures for the individual items of the chunk payload which may be generated by the single instance storage device.