Two decades ago, the first application of surface plasmon resonance phenomenon (SPR) was presented; from then on the improvement on the sensor instrumentation is the key factor for the system accuracy, opening infinity of derived applications of the new optoelectronics sensors investigation. The high specificity surface plasmon resonance sensor presented is based on two photodiode arrays, one for referential measurement and other for the selective detection of substance. This report shows several solutions that contribute to the optimization of the design of electronic acquisition that treats weak signals in noisy electronic media. The design improvements are based on the minimization of the noise in electronic circuits versus digital signal processing limitations. This work solves the inherent problems in circuits design where photodiodes arrays and analog multiplexer are used by means of the dynamic control of the high gain amplifiers chain offsets in transimpedance classic configuration, in the good adjustment of the ADC measurement spectrum bandwidth and in the compensation in real time, with electronic circuits, of the optical noise effects, as dark currents. This optimization is reached after parameterize the process by means of the device self-calibration that will allow to improve the fidelity of the measures notably, this is essential when the variations of the plasmon sensor refraction index to detect has an order of 1e-6.