Microbial electrochemical system (MES) offers sustainable solutions for environmental applications such as wastewater treatment, energy generation, and chemical synthesis by leveraging microbial metabolism and electrochemical processes. This review explores the transformative role of 3D printing in MES research, focusing on reactor body design, electrode fabrication, and bioprinting applications. Rapid prototyping facilitated by 3D printing expedites MES development while unlocking design flexibility, which enhances performance in optimising fluid dynamics and mass transfer efficiency. Tailored ink materials further improve the conductivity and biocompatibility of electrodes, paving the way for environmental applications. 3D-printed bio-anodes and bio-cathodes offer enhanced electrogenesis and boosted electron acceptance processes, respectively, by fine-tuning electrode architectures. Additionally, 3D bioprinting presents opportunities for scaffold fabrication and bioink formulation, enhancing biofilm stability and electron transfer efficiency. Despite current challenges, including material selection and cost, the integration of 3D printing in MES holds immense promise for advancing energy generation, wastewater treatment, resource recovery, carbon utilisation, and biosensing technologies.