A system and method for managing data deduplication of a storage system utilizing persistent consistency point images (PCPIs). Once a target PCPI of a data transfer is generated, a backup management module of the storage system alerts a data deduplication module to begin deduplication of the data contained within the target PCPI. Once the deduplication procedure has been completed, the active file system of the storage system has been deduplicated, however, the target PCPI remains un-deduplicated. In response, the backup management module generates and exports a revised target PCPI. The previous target PCPI may then be deleted, thereby transitioning the exported PCPI's image of the state of the file system to a deduplicated state.