With the technological advances in 3D printing technology, which are associated with ever-increasing printing resolution, additive manufacturing is now increasingly being used for rapid manufacturing of complex devices including microsystems development for laboratory applications. Personalized experimental devices or entire bioreactors of high complexity can be manufactured within few hours from start to finish. This study presents a customized 3D-printed micro bubble column reactor (3D-µBCR), which can be used for the cultivation of microorganisms (e.g., Saccharomyces cerevisiae) and allows online-monitoring of process parameters through integrated microsensor technology. The modular 3D-µBCR achieves rapid homogenization in less than 1 s and high oxygen transfer with kLa values up to 788 h−1 and is able to monitor biomass, pH, and DOT in the fluid phase, as well as CO2 and O2 in the gas phase. By extensive comparison of different reactor designs, the influence of the geometry on the resulting hydrodynamics was investigated. In order to quantify local flow patterns in the fluid, a three-dimensional and transient multiphase Computational Fluid Dynamics model was successfully developed and applied. The presented 3D-µBCR shows enormous potential for experimental parallelization and enables a high level of flexibility in reactor design, which can support versatile process development. © 2021, The Author(s).