This paper proposes low cost reconfigurable embedded back-end architecture for high speed data acquisition, noise cleaning and real time display for a photoacoustic based continuous noninvasive blood glucose monitoring system to combat deadly Diabetes. The signal to noise ratio (SNR) improvement of repeated photoacoustic signal is accomplished by the coherent averaging with trigger unit added as intellectual property (IP) core to the embedded back-end. The maximum sampling speed of the analog to digital converter (ADC) AD9265 interfaced with the embedded system is 125 MSPS which supports digitization of the signal in real-time. The architecture for embedded back-end has been implemented using XC2VP-30-7FF896VIRTEX-II PRO device and the result of the proposed architecture is displayed on LCD in real-time.