In combination with fluidic systems, fluorescence detectors have a large variety of applications e.g. in biomedicine for ph-sensoring or the characterization of chemical reaction processes. Highly integrated and miniaturized optofluidic microsystems enable the handling of very small sample volumes in so-called segmented flow systems, which is beneficial for the practical application. A single-channel fluorescence sensor using planar integrated free space optical systems has been developed in the past. In order to increase the measuring flexibility and accuracy the extension to a multi-wavelength and multi-channel sensor system based on this concept is currently investigated. We present the concept, optical design and fabrication strategy of a highly integrated free space optical fluorescence detector for the application in a segmented-flow environment. The performance of the system is characterized and the application as a biochemical analysis system is discussed.