Because of the delicate biological function of certain substances in the pharmaceutical and life science industry, some established automated joining processes are not applicable for various innovative micro fluidic products. The utilization of heat or ultrasound for bonding can interfere with chemicals and alter their functions. Significant advantages for micro fluidic cartridges include the volume reduction of expensive substances as well as the integration of functionalities such as sensing and dosing in a very small footprint. Hybrid micro fluidic cartridges consisting of different materials like thermoplastics, glass and silicon are typically such devices excluding the use of common automated assembling processes because of their sensitive bio-molecular coatings. Based on conventional robotic equipment, we have developed an innovative process to automatically assemble hybrid micro fluidic components using double-sided adhesive tape. This method allows a cost-effective and reliable production of micro fluidic cartridges since it is based on a standard industrial robot system. The complete process is realized at room temperature so that all biological functions are fully preserved. We have demonstrated experimentally that handling and hybrid bonding of micro fluidic parts of different materials can be automated using standard robotic equipment and dedicated tools, thus allowing a cost-effective and high quality production of micro fluidic systems.