Accurate prediction of lithium-ion batteries’ (LIBs) state-of-health (SOH) is crucial for the safety and maintenance of LIB-powered systems. This study addresses the variability in degradation trajectories by applying gated recurrent unit (GRU) networks alongside principal component analysis (PCA), Granger causality, and K-means clustering to analyze the relationships between operating conditions—such as temperature and load profiles—and battery performance degradation. This paper uses a publicly accessible dataset derived by aging three prismatic LIB cells under a realistic forklift operation profile. First, we identify the features that are relevant to driving variance, then we employ the winning algorithm of K-means clustering for the classification of operational states. Granger causality later investigates the inter-group relationships. Our GRU-BPP model achieves an RMSE value of 0.167 and an MAE of 0.129 for the reference performance testing (RPT) dataset and an RMSE of 0.032 with an MAE of 0.025 for the aging dataset, thus outperformed benchmark methods such as GRU, LME, and XGBoost. These results further enhance the predictiveness and robustness of this approach and yield a holistic solution to the conventional challenges in battery management and their remaining useful life (RUL) predictions.