A method is presented for estimating frequency responses of multiple-input multiple-output bare-airframe dynamics from flight test data containing feedback control and/or mixing of control effectors. Orthogonal phase-optimized multisines are used to simultaneously excite each input with unique harmonic frequencies, at which frequency responses are computed as ratios of output-to-input Fourier transform data. The confounding effects of feedback and mixing are resolved by interpolation of the frequency responses. The analysis can be run in batch for post-flight analysis, or in real time as the aircraft is flying. The effectiveness of the method was verified using simulations of the subscale T-2 generic transport airplane with rate feedback. The method was also demonstrated using flight test data from the X-56A MUTT aeroelastic airplane, which was flown with both feedback control and mixing.