A low-cost seismic instrumentation system (LCSIS) was successfully developed and validated for structural health monitoring (SHM) of three Chilean buildings: the Penuelas Tower, the Santa Marta Building, and the Serena Building. The LCSIS integrates RaspberryShake® RS4D accelerographs connected through a local network managed by a Raspberry Pi 4B (RPi4B), which functions as an NTP server to ensure precise time synchronization, enables remote access, and periodically estimates the building’s dynamic properties using horizontal geophone velocity records processed via the Frequency Domain Decomposition (FDD) method. To account for environmental influences on structural behavior, the LCSIS was coupled with a temperature and relative humidity monitoring unit, later upgraded with a BME280 sensor for continuous ambient data acquisition. The system is powered by a traditional UPS and an industrial PoE switch, ensuring uninterrupted operation during electrical outages. The article presents the main aspects of implementing a low-cost seismic instrumentation system (LCSIS) using RS4D devices. Its performance was verified through shake table tests, showing strong consistency with conventional instrumentation for frequencies below 25–30 Hz. Ambient vibration data are automatically processed on an hourly basis, enabling continuous tracking of the temporal evolution of the dynamic properties. The LCSIS has proven effective in recording multiple seismic events, and the identification of dynamic properties corresponding to the two study cases.