Bitter peptides are short amino acid chains that produce a bitter taste. These peptides are made primarily in food processing through the chemical reduction of peptides. The bitterness arises from the specific sequence of amino acids in peptides, which interact with the bitter taste receptors on the human tongue. These peptides influence nutrition and health, offering insights into protein digestion and bioactive advantages. Hence, correctly identifying bitter peptides is pivotal for revealing the biochemical properties of efficient medication. The computational approach is most suitable for identifying bitterness, where most studies obtained insufficient outcomes. Therefore, the current study developed an ensemble-based framework called “BitterEN”, where we integrate the Gradient Boosting (GB) and Multi-layer Perception (MLP) methods. Our proposed method improved more than 3 % of accuracy compare to all of the state-of-the-arts methods, where the proposed approach achieved 0.995 accuracy in merged feature extractions with the Random Forest (RF) feature selection method. We used 50 iterations over the performance evaluation phases to enable a more exact generalization of model performance. In addition, we provided a convenient GitHub-based version of our bitter peptide identification. It highlights the practical applicability of these findings. We are optimistic that the proposed approach might benefit many fields, including healthcare development and nutritional science.