Raw or unencrypted data is encrypted using a standard encryption algorithm and stored in a Flash memory array. The raw or unencrypted data may be pre-processed before it is encrypted. Pre-processing may include data scrambling, pre-encryption data mixing, or both. Data scrambling may involve an invertible transformation. The scrambled data may then be used to seed a sequence generator. Each output from the sequence generator may be processed using a bit-by-bit Exclusive Or (XOR) operation to impart random or pseudorandom statistical properties. Pre-encryption data mixing may combine the scrambled (or unscrambled) data with information that is unique to each chunk of data, as well as with a user-supplied secret key. This helps ensure that identical raw data chunks are not stored as identical encrypted data chunks in the Flash memory array.