The present disclosure provides for defragmenting deduplicated data, such as one or more backup image files, stored in a deduplicated data store. A defragmentation module can be implemented on a deduplication server to reduce fragmentation of backup images and improve processing time for restoring a backup image. A defragmentation module can be configured to defragment a backup image file by migrating portions of data of the backup image file that are stored in various containers at non-contiguous locations throughout deduplicated data store. A defragmentation module can contiguously write the portions to one or more containers, which are stored at one or more new locations in the deduplicated data store. A defragmentation module can be configured to evaluate whether portions of a backup image file meet criteria for defragmentation. A defragmentation module can also be configured to update location information about the portions that are migrated to the new container(s).