Microbial electrochemical systems (MES) are a relatively new electrochemistry research field and hold great potential for various applications by taking advantage of the metabolic diversity of microorganisms and the flexibility of electrochemical techniques. During the past few decades, a large variety of interesting and novel applications such as energy-generating wastewater treatment, bioelectrochemical CO2 fixation and transformation, bioelectrochemical hydrogen synthesis, desalination, and waste heating energy harvesting have been demonstrated. Meanwhile, multidisciplinary research to improve the performance/efficiency of MES is attracting widespread interest. In the light of deeper understanding of MES through chemistry and biology studies, new interdisciplinary chemical biotechnology research taking advantage of both disciplines is emerging and becoming a hot research topic in this area. In this chapter, the great contributions of chemical bioengineering to MES are highlighted. In particular, augmentation of extracellular electron transfer between bacteria and the electrode by chemicals, conductive polymers, and carbon nanomaterials are reviewed. Moreover, other chemical bioengineering approaches to improve MES through manipulation of cell physiology, such as by surfactant and metal ion treatment, quorum sensing signaling modulation, and cell immobilization, are also emphasized. Future directions for chemical bioengineering of MES are also discussed.