A simple and robust nanolithographic method, that allows sub-100 nm chemical patterning on a range of oxide surfaces, was developed in order to fabricate nanoarrays of plant light harvesting LHCII complexes. The site-specific immobilization and the preserved functionality of the LHCII complexes were confirmed by fluorescence emission spectroscopy. Nanopatterned LHCII trimers could be reversibly switched between fluorescent and quenched states by controlling the detergent concentration in the imaging buffer. A three-fold quenching of the average fluorescence intensity was accompanied by a decrease in the average (amplitude weighted) fluorescence lifetime from approximately 2.24 ns to approximately 0.4 ns, attributed to the intrinsic ability of LHCII to switch between fluorescent and quenched states upon changes in its conformational state. The nanopatterning methodology was extended by immobilizing a second protein, the enhanced Green Fluorescent Protein (EGFP), onto LHCII-free areas of the chemically patterned surfaces. This very simple surface chemistry, which allows simultaneous selective immobilization and therefore sorting of the two types of protein molecules on the surface, is a key underpinning step towards the integration of LHCII into switchable biohybrid antenna constructs.