Structural Health Monitoring (SHM) is a process where, through sensors-based electronic systems and output data analysis, the structural integrity of a building or an infrastructure is observed and determined through periodically sampled measurements for material and geometric variations, ensuring safety and minimizing risk factors. Over the years, the approach to this problem evolved both in terms of system technology, with the use of more accurate sensors, and the parameters used to determine the building status, i.e., the extraction of the damage index. In these terms, structural modal harmonics-based analysis is acquiring more and more relevance. In this paper, we propose a fully custom master multi-slave system used for SHM purposes, capable of acquiring data from six different channels coming from two independent accelerometers suitably configured as to synchronously produce spectrograms and static trim of the monitored structure. A test of the system has been performed on a modular structure subject to random perturbation. Time and frequency domain results were analyzed before and after structural alterations. Their effects were studied in a 500 Hz bandwidth, showing a drift in the resonant frequency of the structure from 145 Hz to 152 Hz, and, additionally, a harmonic displacement: medium-frequency components experienced a 50 Hz drift, while low-frequency components collapsed into two harmonics at 60 Hz and 90 Hz. These tests proved the system’s functionality and the feasibility of this method for structural integrity analysis and, eventually, damage evaluation.