Multivariable disturbance accommodated observer based control (DOBC) scheme is presented to mitigate loads generated due to wind shear and tower shadow using individual blade pitch for above-rated wind speed condition of wind turbine. Wind shear and tower shadow add flickers as 1p, 3p, 6p and so on, (p is the rotor rotational frequency) for three-bladed wind turbine. Novel DOBC with individual pitch control (IPC) to mitigate the flickers is presented and linear state-space model of wind turbine with tower dynamics is developed. The proposed controller is tuned using optimal control theory to reduce fatigue of drive-train, tower and to regulate output power. The authors have tested the controller on NREL's 5 MW wind turbine, FAST (fatigue, aerodynamics, structures and turbulence) code is used for load modelling and MATLAB/Simulink is used for the simulation. A comparison of power spectral density of generator speed, drive-train torsion and tower fore-aft moment shows better mitigation to the flickers by proposed controller as compared with proportional–integral (PI) and disturbance accommodation control (DAC) with collective pitch control. Furthermore, it shows less degradation in the performance as moving away from the operating point for above-rated wind speed condition of wind turbine. It is concluded that proposed multivariable controller shows better mitigation to turbulent and cyclic aerodynamic loads, provide better regulation to output power using IPC of wind turbine and increased the lifetime of drive-train torsion and tower as compared with PI and DAC.