The synthesis of bifunctional mesoporous silica nanoparticles is described. Two chemically orthogonal functionalities are incorporated into mesoporous silica by co-condensation of tetraethoxysilane with two orthogonally functionalized triethoxyalkylsilanes. Post-functionalization is achieved by orthogonal surface chemistry. A thiol–ene reaction, Cu-catalyzed 1,3-dipolar alkyne/azide cycloaddition, and a radical nitroxide exchange reaction are used as orthogonal processes to install two functionalities at the surface that differ in reactivity. Preparation of mesoporous silica nanoparticles bearing acidic and basic sites by this approach is discussed. Particles are analyzed by solid state NMR spectroscopy, elemental analysis, infrared-spectroscopy, and scanning electron microscopy. As a first application, these particles are successfully used as cooperative catalysts in the Henry reaction.