Structural health monitoring (SHM) and damage detection using vibration-based methods continue to be of interest in fields such as civil and mechanical engineering, among others. Early identification of damage can save human lives and facilitate low-cost recovery of existing infrastructure. The methods used in SHM can have a local or global approach. A local approach checks the components of the structure in detail, while a global approach detects general changes in the characteristics of the structure. In this article, a methodology with a global approach is proposed, which combines the properties of empirical mode decomposition (EMD), synchronized wavelet transform (SWT), and spline interpolation, with the aim of identifying modal properties and damage. In this methodology, it is possible to identify the frequency content of a signal over time; if there are changes in the modal properties of the structure, it is known that there were changes in the physical properties; therefore, there was damage in the structure. To validate the effectiveness of the proposed methodology, the instant of damage is identified, as well as the natural frequencies of the Benchmark Phase I, considering the structure without damage and with damage due to loss of stiffness in the first and third floors. The analyzed signal is created considering the undamaged and damaged states of the structure. First, the instant of damage and the change in the natural frequencies of the structure due to stiffness loss damage were identified using the SWT. Subsequently, the proposed methodology was validated by comparing the values obtained in the identification of the natural frequencies with the values reported by other authors. The minimum and maximum errors were 0.0% and 2.31%, respectively, compared to the results reported by the AISCE-ASCE group. The proposed methodology proved to be robust as a SHM method; it identifies frequencies with closely spaced modes and does not require a priori knowledge of the structure.