The development of Li-ion battery energy storage systems is crucial for climate change mitigation and the expansion of electromobility infrastructure. Despite their high energy density, Li-ion cells generate significant heat during intensive operation, which can accelerate degradation or trigger thermal runaway. This study investigates the use of cost-effective, organic, dielectric Phase Change Materials (PCMs)—based on paraffin 42-44, soy wax, and beeswax—to enhance the thermal management of LFP (Lithium Iron Phosphate) cells. The PCMs were characterized using Differential Scanning Calorimetry (DSC) to determine specific heat, heat capacity, and phase transition temperatures. Molecular structures were analyzed via Scanning Electron Microscopy (SEM) and Raman spectroscopy. Thermal conductivity was measured using the Hot Disk method (ISO 22007) to empirically derive thermal diffusivity. Test modules in a 3s1p configuration were fabricated using 3D-printed molds and PCM encapsulation. Experimental results under high current loads (up to 20C) demonstrated that full PCM immersion reduced peak cell temperatures by approximately 20°C, maintaining surface temperatures below 42°C. Advanced thermographic analysis, performed using FLIR Research Studio PRO and MATLAB, employed internal morphological semi-gradient edge segmentation. This approach optimized PCM volume and cell spacing based on thermal diffusivity distribution. To assess the PCM's impact on the State of Energy (SoE), electrical parameters were identified via Hybrid Pulse Power Characterization (HPPC). Cell dynamics were represented by a second-order Thevenin equivalent circuit model. Parameters were identified using the Levenberg-Marquardt algorithm, and model accuracy was validated using Mean Squared Error (MSE) and Normalized Root Mean Square Error (NRMSE) across the full State of Charge (SoC) range. The findings confirm that bio-based PCMs provide a safe and efficient solution for compact energy storage in small electric vehicles.