Covalent functionalization of graphene oxide (GO) with boron dipyrromethenes (BODIPYs) was achieved through a facile synthesis, affording two different GO-BODIPY conjugates where the main difference lies in the nature of the spacer and the type of bonds between the two components. The use of a long but flexible spacer afforded strong electronic GO-BODIPY interactions in the ground state. This drastically altered the light absorption of the BODIPY structure and impeded its selective excitation. In contrast, the utilisation of a short, but rigid spacer based on boronic esters resulted in a perpendicular geometry of the phenyl boronic acid BODIPY (PBA-BODIPY) with respect to the GO plane, which enables only minor electronic GO-BODIPY interactions in the ground state. In this case, selective excitation of PBA-BODIPY was easily achieved, allowing to investigate the excited state interactions. A quantitative ultrafast energy transfer from PBA-BODIPY to GO was observed. Furthermore, due to the reversible dynamic nature of the covalent GO-PBA-BODIPY linkage, some PBA-BODIPY is free in solution and, hence, not quenched from GO. This resulted in a weak, but detectable fluorescence from the PBA-BODIPY that will allow to exploit GO-PBA-BODIPY for slow release and imaging purposes.