Herein, we describe the construction of a novel dual-pad referencing surface plasmon resonance (SPR) sensor utilizing electrolytic grafting of diazonium salts to individually functionalize two gold pads positioned in a single fluidic channel. Using a dove prism, a simple single axis optical train may be employed without compromising the analytical performance. Once functionalized, one pad is used as the analytical sensing pad for detection of molecular interactions while the other serves as the reference pad, compensating for background refractive index fluctuations. The reference pad effectively compensates bulk refractive index changes and temperature variations as well as other nonspecific effects. The sensor was applied to calibration of a pH-responsive polymer layer in the presence of bulk refractive index and temperature variations. Monitoring selective attachment of a protein is also demonstrated. To our knowledge, this is the first implementation of in-channel referencing SPR sensor utilizing diazonium salt-based surface chemistry.