Accurate and early prediction of diabetes is crucial for initiating prompt treatment and minimizing the risk of long-term health issues. This study introduces a comprehensive machine learning model aimed at improving diabetes prediction by leveraging two clinical datasets: the PIMA Indians Diabetes Dataset and the Early-Stage Diabetes Dataset. The pipeline tackles common challenges in medical data, such as missing values, class imbalance, and feature relevance, through a series of advanced Preprocessing steps, including class-specific imputation, engineered feature construction, and SMOTETomek resampling. To identify the most informative predictors, a hybrid feature selection strategy is employed, integrating recursive elimination, Random Forest-based importance, and gradient boosting. Model training uses Random Forest and Gradient Boosting classifiers, which are fine-tuned and combined through weighted ensemble averaging to boost predictive performance. The resulting model achieves 93.33% accuracy on the PIMA dataset and 98.44% accuracy on the Early-Stage dataset, outperforming previously reported approaches. To enhance transparency and clinical applicability, both local (LIME) and global (SHAP) explainability methods are applied, highlighting clinically relevant features. Furthermore, probability calibration is performed to ensure that predicted risk scores align with true outcome frequencies, increasing trust in the model’s use for clinical decision support. Overall, the proposed model offers a robust, interpretable, and clinically reliable solution for early-stage diabetes prediction.