Standalone photovoltaic systems play an important role in providing reliable renewable energy in remote areas. These systems depend heavily on battery energy storage, especially lithium iron phosphate batteries, which are known for their safety and long cycle life. However, battery degradation remains a major challenge, as high charging currents, temperature variations, and wide state-of-charge fluctuations introduce electro-thermal stress that reduces the useful lifetime of the storage system. To address this issue, this paper presents a Flexible Power Point Tracking (FPPT) strategy supported by a fuzzy-logic-based controller. In this context, battery stress refers to the combined electrochemical and thermal stress induced by high charging currents, elevated operating temperatures, and large state-of-charge (SOC) excursions, which are known to accelerate ageing mechanisms and capacity fade. Based on a review of the existing literature, most FPPT and lifetime-oriented control studies have focused on lithium-ion batteries such as NMC or LCO chemistries, while limited attention has been given to lithium iron phosphate (LiFePO4) batteries. The goal is to limit battery stress by reducing current peaks, mitigating temperature rise, and smoothing state-of-charge variations, thereby improving battery lifetime without compromising the stability of the standalone PV system. A complete PV–battery model is developed in PLECS and tested using one-year irradiance, temperature, and load data from Perth, Australia. The results show that the FPPT–Fuzzy controller reduces current peaks, stabilizes the state of charge, and lowers the thermal impact on the battery when compared with traditional MPPT. As a result, overall degradation decreases and the battery lifetime is extended by approximately 7%. These findings demonstrate that FPPT is a promising method for improving the long-term performance of renewable energy systems based on lithium iron phosphate battery storage.