Abstract The paper deals with a novel modified backstepping algorithm to ensure the stability of the nonlinear multiple-input multiple-output plant under unknown bounded parametric uncertainties, Lipschitz nonlinear disturbances, and cross-couplings. The modification is based on the auxiliary loop method that permits to estimate undesired dynamics as disturbances and suppress them. High robustness of the closed-loop system without using high-gain components is achieved. The ractical contribution of the results is demonstrated using laboratory platform ”Twin Rotor MIMO System”.