The preservation of the bioreactivity of antibodies and proteins by immobilization on the surface of magnetic nanoparticles is essential for particle targeting applications in diagnosis and therapy. Here we compare the conjugation of a model antibody and of streptavidin to the surface of biocompatible 100 nm magnetic starch nanoparticles by strain-promoted alkyne-azide cycloaddition (SPAAC) with the established carbodiimide and maleimide chemistry. Under our reaction conditions the bioreactivity of the immobilized antibody was about 28% for the random amide bond formation using carbodiimide chemistry, the bioreactivity increased to about 61% for bioorthogonal SPAAC and to about 90% for maleimide conjugation. The same order was found for the biotin binding capacity of streptavidin, that was conjugated to the magnetic nanoparticles with the same methods. The described analytical methods are a platform for further studies with improved bioorthogonal conjugation reactions, e.g. the strain-promoted alkyne-nitrone cycloaddition (SPANC).