One challenge for current surface acoustic wave (SAW) biosensors is reducing nonspecific adsorption. A device propagating Rayleigh and shear horizontal surface acoustic waves in orthogonal directions fabricated in ST quartz has the capability of achieving simultaneous detection and nonspecific binding (NSB) protein removal. Current measurement methods for a SAW sensor system based on this device require large-size and expensive equipment such as a vector network analyzer (VNA), signal generator, and frequency counter, which are not suitable for portable, especially point-of-care, applications. In this work, a portable platform based on a direct digital synthesizer (DDS) is investigated for the orthogonal SAW sensor, integrating signal synthesis, gain control, phase/amplitude measurement, and data processing in a small, portable electronic system. This prototype was verified for both stability and repeatability, and the results matched very well with VNA measurements. Finally, system performance in real-time sensing and NSB removal was evaluated.