Advances in the instrumentation and materials for photopolymerization 3D printing aided the use of this powerful technique in the fabrication of microfluidic devices. The costs of printers and supplies have been reduced to the point where this technique becomes attractive for prototyping microfluidic systems with good resolution. With all the development of multi-material 3D printers, most of the microfluidic devices prepared by photopolymerization 3D printing are based on a single substrate material. We developed a digital light processing multi-material 3D printer where two or more resins can be used to prepare complex objects and functional microfluidic devices. The printer is based on a vat inclination system and embedded peristaltic pumps that allow the injection and removal of resins and cleaning step between material changes. Although we have built the whole system, the modification can be incorporated into commercially available printers. Using a high-resolution projector, microfluidic channels as narrow as 43 μm were obtained. We demonstrate the printing of multi-material objects containing flexible, rigid, water-soluble, fluorescent, phosphorescent, and conductive (containing PEDOT or copper nanoparticles) resins. An example of a microfluidic chip containing electrodes for electrochemical detection is also presented.