Example implementations relate to metadata operations in a storage system. An example includes a storage controller loading a manifest from persistent storage into memory, and loading a first container index from persistent storage into the memory. The first container index is associated with the manifest loaded into the memory. The storage controller determines whether a tracking data structure of the first container index includes an identifier of the manifest. In response to a determination that the tracking data structure of the first container index does not include the identifier of the manifest, the storage controller discards the manifest.