The parameters of a second order integrator plus delay model are estimated in the frequency domain. The independence of the Fourier transform amplitude to time delay changes and the Levi (1959) manipulation of the least square estimator are utilized to obtain a linear estimator problem. The obtained model is matched around the critical frequency. The method is applicable to both under- and over-damped closed loops. Therefore it is suitable for the purpose of the controller tuning. Simulations of an actual second order integrating process and a condenser water level dynamics are used to demonstrate the application of the method.