Photonic systems are gaining an important role in the field of medical diagnosis due to the achievable high sensitivity and selectivity and low cost, enabling the fabrication of disposable point of care diagnosis systems for multiple pathologies. In this work we present the detector subsystem developed for a multi-channel surface plasmon resonance (SPR) based sensor. The core of the system is a multimode interferometer splitter, fabricated in amorphous silicon, followed by multiple sensitive SPR structures with a functionalized gold layer that modulate the transmitted light waves, in the presence of the biomarker, which are then detected by infrared detectors. For this purpose a highly adaptable detection system based on a InGaAs line CCD device was developed. The IR sensor used in the prototype has 128 (50 x 250 μm) pixels but other formats are supported. To adapt to different light guiding structures, the CCD pixels can be combined forming multiple detection channels. Optical sensor configuration and readout operations are performed trough a USB connection using the SCPI standard. The system includes an analog front end with a programmable gain amplifier and offset adjustment followed by a fast analog to digital converter feeding the data to a STM32 family processor. A computer application was also developed for system configuration and signal readout and storage. The testing results from the complete system are presented. Documentation of the developed system is provided for third party use, all the material generated within this work is available online in a repository.