Intercalated metal-organic frameworks (iMOFs) based on aromatic dicarboxylate are appealing negative electrode active materials for Li-based electrochemical energy storage devices. They store Li ions at approximately 0.8 V vs. Li/Li⁺ and, thus, avoid Li metal plating during cell operation. However, their fast-charging capability is limited. Here, to circumvent this issue, we propose iMOFs with multi-aromatic units selected using machine learning and synthesized via solution spray drying. A naphthalene-based multivariate material with nanometric thickness allows the reversible storage of Li-ions in non-aqueous Li metal cell configuration reaching 85% capacity retention at 400 mA g⁻¹ (i.e., 30 min for full charge) and 20 °C compared to cycling at 20 mA g⁻¹ (i.e., 10 h for full charge). The same material, tested in combination with an activated carbon-based positive electrode, enables a discharge capacity retention of about 91% after 1000 cycles at 0.15 mA cm⁻² (i.e., 2 h for full charge) and 20 °C. We elucidate the charge storage mechanism and demonstrate that during Li intercalation, the distorted crystal structure promotes electron delocalization by controlling the frame vibration. As a result, a phase transition suppresses phase separation, thus, benefitting the electrode’s fast charging behavior.