Rapid growth of smart electronics and implantable medical devices markets has driven the development of next-generation sustainable, flexible, or implantable batteries. Conducting polymers with unique mechanical and electronic properties offer new possibilities and have attracted great attention. In this review, we discuss approaches used to tune conducting polymers at the molecular level for designated properties and applications such as improved electrochemical performance, and we discuss approaches used to tune conducting polymers at the molecular level to enhance selected properties for applications such as lithium/sodium ion batteries, biodegradable electrodes or enhanced solution processability for advanced manufacture of such structures. We provide here insights into the molecular structure-electrochemical performance relationships. Finally, we present perspectives on the further development of conducting polymer materials for these novel batteries.