Techniques are provided for background deduplication using trusted fingerprints. Trusted fingerprints of blocks are inserted into a trusted fingerprint store as the blocks are being allocated by a file system sequentially according to block numbers of the blocks. In this way, the trusted fingerprint store is indexed by block numbers of where the blocks are stored. Blocks that are to be deduplicated are identifying by sorting the blocks based upon weak fingerprints, and moving duplicates to a dup file. The dup file is sorted based upon block numbers. Trusted fingerprints are loaded from the trusted fingerprint store for deduplicating the blocks within the dup file.