Sun-induced chlorophyll fluorescence (Fs) is a promising parameter for remote measuring plant photosynthesis. It has been demonstrated that Fs at cell and leaf level is strongly related to photosynthesis. The transfer of the Fs approach to canopy level remains challenging as the canopy Fs signal is not fully understood yet. Several factors influence the Fs signal and need to be quantified. However, the absence of dedicated imaging spectrometers limits the experimental data for such investigations. We propose an experimental setup allowing spatio-temporal investigations of canopy Fs. A non-imaging spectrometer was installed in a low-flying aircraft. An agricultural area was continuously monitored including the extensive coverage of dedicated fields. Fs was retrieved from spectrometer data using the FLD (Fraunhofer Line Depth) method combined with simulated (MODTRAN-4) at-sensor radiances of a reference surface. We present the methodological framework to derive canopy chlorophyll fluorescence from airborne based non-imaging spectrometer measurements and a quality assessment of the data.