Modal operational analysis methods are procedures to identify modal parameters of structures from the response to unknown random excitations existing on buildings and in machines during operation. In many practical cases, in addition to the random loads, harmonic excitations are also present due for instance to rotating components. If the frequency of the harmonic component of the input is close to an eigenfrequency of the system, operational modal analysis procedures fail to identify the modal parameters accurately. Therefore, we propose a modification of the least-square complex exponential identification procedure to include explicitly the harmonic component. In that way, the modal parameters can be identified properly. We illustrate the efficiency of the proposed approach on the example of a beam structure excited by multi-harmonic loads superposed on random excitation.