Boron-doped diamond (BDD) electrodes are well known for the in situ production of strong oxidants. These antimicrobial agents are produced directly from water without the need of storage or stabilization. An in situ production of reactive oxygen species (ROS) used as antimicrobial agents has also been used in recently developed medical applications. Although BDD electrodes also produce ROS during water electrolysis, only a few medical applications have appeared in the literature to date. This is probably due to the difficulties in the miniaturization of BDD electrodes, while maintaining a stable and efficient electrolytic process in order to obtain a clinical applicability. In this attempt, a cannula-based electrode design was achieved by insulating the anodic diamond layer from a cathodic cannula, using a second layer of non-conducting diamond. The undoped diamond (UDD) layer was successfully grown in a spotted pattern, resulting in a perfectly insulated yet still functional BDD layer, which can operate as a miniaturized flow reactor for medical applications. The spotted pattern was achieved by introducing a partial copper layer on top of the BDD layer, which was subsequently removed after growing the undoped diamond layer via etching. The initial analytical observations showed promising results for further chemical and microbial investigations.