An on-line estimation technique of multiple-frequency oscillatory forces combined with the Hilbert–Huang transform for an important class of actively controlled, forced vibrating mechanical systems with nonlinear stiffness forces is proposed. Polynomial parametric nonlinearities are incorporated in the significantly perturbed vibrating system dynamics. This class of nonlinear vibrating systems can exhibit harmful large-amplitude vibrations, which are inadmissible in many engineering applications. Disturbing oscillations can be also provoked due to interactions of the primary mechanical system to be actively protected against dangerous vibrations with other forced uncertain multidegree-of-freedom nonlinear vibrating systems. Taylor’s series expansion to dynamically model uncertain vibrating forces into a small time window for real-time estimation purposes is employed. Intrinsic mode functions of multiple-frequency vibrating forces can be then obtained by the Hilbert-Huang transform. Uncertain instantaneous frequencies and amplitudes of disturbing oscillations can be directly computed in temporal space. An active vibration control scheme for efficient and robust tracking of prescribed motion reference profiles based on multiple frequency force estimation is introduced as well. The presented closed-loop on-line estimation technique can be extended for other classes of nonlinear oscillatory systems. Analytical, experimental and numerical results to prove the estimation effectiveness are presented. Numerical results show reasonable estimation errors of less than 2%.