Vibration-based structural health monitoring (SHM) of (large) infrastructure through operational modal analysis (OMA) is a commonly adopted strategy. This is typically a four-step process, comprising estimation, tracking, data normalization, and decision-making. These steps are essential to ensure structural modes are correctly identified, and results are normalized for environmental and operational variability (EOV). Other challenges, such as nonstructural modes in the OMA, for example, rotor harmonics in (offshore) wind turbines (OWTs), further complicate the process. Typically, these four steps are considered independently, making the method simple and robust, but rather limited in challenging applications, such as OWTs. Therefore, this study aims to combine tracking, data normalization, and decision-making through a single machine learning (ML) model. The presented SHM framework starts by identifying a “healthy” training dataset, representative of all relevant EOV, for all structural modes. Subsequently, operational and weather data are used for feature selection and a comparative analysis of ML models, leading to the selection of tree-based learners for natural frequency prediction. Uncertainty quantification (UQ) is introduced to identify out-of-distribution instances, crucial to guarantee low modeling error and ensure only high-fidelity structural modes are tracked. This study uses virtual ensembles for UQ through the variance between multiple truncated submodel predictions. Practical application to monopile-supported OWT data demonstrates the tracking abilities, separating structural modes from rotor dynamics. Control charts show improved decision-making compared to traditional reference-based methods. A synthetic dataset further confirms the approach’s robustness in identifying relevant natural frequency shifts. This study presents a comprehensive data-driven approach for vibration-based SHM.