Pendulum tuned mass dampers (PTMDs) have been employed in several full-scale applications to attenuate excessive structural motions, which are mostly due to wind. Conducting periodic condition assessments of the devices to ascertain their health is necessary to ensure their continued optimal performance, which involves identifying the modal parameters of the underlying (bare) structure to which they are tuned to. Such an identification is also necessary for the design of control systems such as adaptive tuned mass dampers. Existing methods of arresting the motion of the damper to estimate the modal properties are expensive, time-consuming, and not suitable for online tuning. Instead, in this paper, parameter estimation using the Extended Kalman Filter (EKF) is proposed to undertake this task. The central task accomplished here is to estimate the dynamic characteristics of the bare structure (structure without the PTMD) from response measurements of the coupled main structure and PTMD system. The proposed methodology relies on ambient acceleration measurements of TMD-attenuated responses to estimate the bare structural modal frequencies, damping, and mode shapes, which can then be used either for condition assessment or for control. The application of EKF to modal parameter estimation is not new. However, a methodology to address the problem in wind engineering arising from stochastic disturbances present in both the measurement and state equations, and unknown process and noise covariances arising due to ambient excitations, is presented for the first time. Extensively studied for synthetic data, these two challenges have limited thus far the application of Kalman filtering to practical wind engineering parameter estimation problems using experimentally obtained measurements. In this paper, a detailed methodology is presented to address these challenges by using a modified form of the standard EKF equations, together with an algorithm to estimate the unknown disturbance and measurement noise covariances. Numerical simulations and an experimental study are both presented. Results demonstrate that the method proposed provides reliable estimates for the modal parameters required to perform condition assessment and control tasks for pendulum tuned mass dampers.