Buildings constructed with cross-laminated timber (CLT) panels have been gaining international interest in recent years, mainly due to their sustainability and industrialization attributes. However, there are still doubts about the stability of the dynamic properties of this type of building over time, as wood undergoes dimensional changes due to variations in temperature and relative humidity. The objective of this study is to evaluate the variability of the dynamic properties of a 5-story CLT building prototype over 2 years. The dynamic properties of the CLT building were estimated through a 2-stage process. In the first stage, accelerometers were installed on various floors of the building, and the vibrations induced by the environment were recorded 96 times a day over a two-year period. Then, in the second stage, each acceleration record was processed using the Stochastic Subspace Identification method (SSI) to estimate the two fundamental frequencies of lateral vibration of the building. The results showed that the lateral frequencies of the CLT building were 9% lower in summer than in winter. This phenomenon correlated positively with measurements of the moisture content of the wood in the CLT walls. In other words, as the moisture content in the CLT panels decreased, volumetric contractions occurred in the panels, and there was less interlocking at the joints between panels, resulting in lower lateral stiffness for the building. These results are expected to contribute to regulatory updates in Chile and to the probabilistic calibration of future numerical models of this building.