Estimation of the dynamic parameters of bearings is essential in order to be able to interpret the performance of rotating machinery. In this paper, we propose a method to estimate the dynamic parameters of the bearings in a flexible rotor system. By utilizing the electromagnetic excitation generated by a built-in PM motor and finite element (FE) modeling of the rotor, safe, low-cost, and real-time monitoring of the bearing dynamics can be achieved. The radial excitation force is generated by injecting an alternating d-axis current into the motor windings. The FE model of the rotor and the measured frequency responses at the motor and bearing locations are used to estimate the dynamic parameters of the bearings. To evaluate the feasibility of the proposed method, numerical simulation and experiments were carried out on a flexible rotor system combined with a bearingless motor (BELM) having both motor windings and suspension windings. The numerical simulation results show that the proposed algorithm can accurately estimate the dynamic parameters of the bearings. In the experiment, the estimates made when utilizing the excitation force generated by the motor windings are compared with the estimates made when utilizing the excitation force generated by the suspension windings. The results show that most of the stiffness and damping coefficients for the two experiments are in good agreement, within a maximum error of 8.92%. The errors for some coefficients are large because the base values of these coefficients are small in our test rig, so these coefficients are sensitive to deviations. The natural frequencies calculated from the dynamic parameters estimated from the two experiments are also in good agreement, within a maximum relative error of 3.04%. The proposed method is effective and feasible for turbomachines directly connected to motors, which is highly significant for field tests.