Structural health monitoring (SHM) is an effective operating technique devoted to enhance the robustness of an infrastructure, and to validate its safety requirements. The aim of SHM is to determine a structure’s reaction when subjected to any type of excitation, by means of identifying modifications in basic vibration measurements and modal parameters such as natural frequencies, damping and mode shapes. Consequently, sensors are mounted on a structure intending to record data on equal time intervals basis prior to, during and after an induced stimulation. Therefore, the necessity to adopt a computer-based data acquisition (DAQ) technique is required in this analytical approach in order to evaluate vibrational signals collected by sensors placed on a structure. In this work an accurate microcontroller-based DAQ system is proposed to monitor a pedestrian bridge located in Athens Greece for the purpose of characterizing the system state and evaluate the modal properties of the investigated structure. Four low-cost yet accurate triaxial accelerometers were systematically placed along the bridge intending to report the system response toward different generated perturbations. The proposed monitoring and computational system was tested in laboratory conditions prior to the bridge assessment. Three triaxial accelerometer were installed on a steel cantilever beam. A comparative analysis between the results of the suggested DAQ system and that of the standard laboratory DAQ system National Instrument DAQ was performed to test the accuracy of the suggested framework.