Systems and methods are described for providing secure storage of data sets while enabling efficient deduplication of data. Each data set can be divided into fixed-length blocks. The plaintext of each block can be convergently encrypted, such as by using a hash of the plaintext as an encryption key, to result in block-level ciphertext that can be stored. If two data sets share blocks, the resulting block-level ciphertext can be expected to overlap, and thus duplicative block-level ciphertexts need not be stored. A manifest can be created to facilitate re-creation of the data set, which manifest identifies the block-level ciphertexts of the data set and a key by which each block-level ciphertext was encrypted. By use of block-level encryption, nearly identical data sets can be largely deduplicated, even if they are not perfectly identical.