Self-assembled monolayers of octadecylphosphonic acid and 16-phosphonohexadecanoic acid (PHDA) were formed on the semiconductor substrates gallium nitride (GaN) and aluminium gallium nitride (AlGaN). The presence of the molecular layers was verified through x-ray photoelectron spectroscopy and ultraviolet photoelectron spectroscopy. Structural information was acquired with infrared spectroscopy which verified the bonding orientation of the carboxyl-containing PHDA. The impact of the molecular layers on the channel conductivity and the surface electronic structure of an AlGaN/GaN heterostructure was measured. Our results indicate that pinning of the surface Fermi level prohibits modification of the channel conductivity by the layer. However, a surface dipole of ∼0.8 eV is present and associated with both phosphonic acid layers. These results are of direct relevance to field-effect-based biochemical sensors and metal–semiconductor contact formation for this system and provide a fundamental basis for further applications of GaN and AlGaN technology in the fields of biosensing and microelectronics.