Silicon photonic devices with either silicon or silicon nitride waveguides have increasingly been used in many applications besides communications, especially as sensors in label-free biosensing, where guided light signals are affected by biorecognition molecules immobilized on the surface. The coating of protein (i.e., bioreceptors) by biochemical process on the waveguide surface is a crucial step in creating a functionalized device that can be used for biosensing. As a conventional method that uses 3-aminopropryltriethoxysilane (APTES) and glutaraldehyde (GA), the APTES-GA method has the limitation of using a GA crosslink, of which the two functional groups can bind to nonspecific proteins, causing irregular binding. In this study, we proposed a new coating technique to avoid such problem by applying APTES silanization with 1-ethyl-3-(3-dimethyl aminopropyl)-carbodiimide (EDC)-N-hydroxysuccinimide (NHS) protein crosslink, denoted by the APTES-(EDC/NHS) method. The EDC/NHS reaction was shown to be able to immobilize protein in ordered orientation due to consistent arrangement between a carboxylic group of protein molecules and an amine group of covalent-linked APTES on surface. By applying APTES silanization, we circumvented the use of hazardous cleaning agent in the conventional EDC/NHS technique. Several surface characterization techniques were carried out to assess and compare the two biocoating techniques, including scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), spectroscopic ellipsometry (SE), and atomic force microscopy (AFM). On silicon, the results of antihuman TNF-alpha antibody coating showed that the proposed APTES-(EDC/NHS) technique has better repeatability in terms of less roughness of the coated protein at 1.5 nm compared with 6.3 nm, due to the ordered arrangement of coated antibody molecules. On a silicon nitride waveguide device, the proposed APTES-(EDC/NHS) technique exhibits dense antibody immobilization on a waveguide in SEM images due to stable amide bond formation via EDC/NHS crosslink mechanism. The specificity of the immobilized antibodies was confirmed by enzyme-linked immunosorbent assays (ELISA), with an average optical density at 450 nm of 0.175 ± 0.01 compared with 0.064 ± 0.009 of negative control. The proposed technique also reduced the overall process time since proteins are crosslinked to the silanized waveguide surface in a single step.