This study presents a novel LSTM–CNN-based adaptive scheduling framework (LSTM-CNN–AS) designed to improve real-time energy management and extend the lifespan of lithium-ion Battery Energy Storage Systems (BESS) in rural and resource-constrained microgrids. In contrast to conventional methods that prioritize economic optimization, the proposed framework incorporates state of health (SOH) aware control and adaptive closed-loop scheduling to enhance operational reliability and battery longevity. The architecture combines Long Short-Term Memory (LSTM) and Convolutional Neural Networks (CNN) for accurate SOH estimation, with lightweight Multi-Layer Perceptron (MLP) models supporting real-time scheduling and state of charge (SOC) regulation. Operational safety is maintained by keeping SOC within 20–80% and SOH above 70%. The proposed model training and validation are conducted using two real-world datasets: the Mendeley Lithium-Ion SOH Test Dataset and the DKA Solar System Dataset from Alice Springs, both sampled at 5-min intervals. Performance is evaluated across three operational scenarios, which are 2C charging with random discharge; random charging with 3C discharge; and fully random profiles, achieving up to 44% reduction in MAE and an R²; score of 0.9767. A one-month deployment demonstrates a 30% reduction in charging time and 40% lower operational costs, confirming the framework’s effectiveness and scalability for rural microgrid applications.