Shuffling is a well-known countermeasure against side-channel attacks. It typically uses the Fisher-Yates (FY) algorithm to generate a random permutation which is then utilized as the loop iterator to index the processing of the variables inside the loop. The processing order is scrambled as a result, making side-channel attacks more difficult. Recently, a side-channel attack on a masked and shuffled implementation of Saber requiring 61,680 power traces to extract the long-term secret key was reported. In this paper, we present an attack that can recover the long-term secret key of Saber from 4,608 traces. The key idea behind the 13-fold improvement is to recover FY indexes directly, rather than by extracting the message Hamming weight and bit flipping, as in the previous attack. We capture a power trace during the execution of the decryption algorithm for a given ciphertext, recover FY indexes 0 and 255, and extract the corresponding two message bits. Then, we modify the ciphertext to cyclically rotate the message, capture a power trace, and extract the next two message bits with FY indexes 0 and 255. In this way, all message bits can be extracted. By recovering messages contained in k∗ l chosen ciphertexts constructed using a new method based on error-correcting codes of length l, where k is the module rank, we recover the long-term secret key. To demonstrate the generality of the presented approach, we also recover the secret key from a masked and shuffled implementation of CRYSTALS-Kyber, which NIST recently selected as a new public-key encryption and key-establishment algorithm to be standardized.