Conducting polymer-based composites have recently becoming popular in both academic research and industrial practices due to their high conductivity, ease of process, and tunable electrical properties. The multifunctional conducting polymer-based composites demonstrated great application potential for in vivo therapeutics and implantable electronics, including drug delivery, neural interfacing, and minimally invasive electronics. In this review article, the state-of-the-art conducting polymer-based composites in the mentioned biological fields are discussed and summarized. The recent progress on the synthesis, structure, properties, and application of the conducting polymer-based composites is presented, aimed at revealing the structure-property relationship and the corresponding functional applications of the conducting polymer-based composites. Furthermore, key issues and challenges regarding the implantation performance of these composites are highlighted in this paper.