Abstract In this study, an adaptive fuzzy extended state observer (AFESO) for single-input–single-output nonlinear affine systems in the presence of external disturbances and output constraints is proposed. In this regard, an extended state observer (ESO) was employed to estimate the unmeasured states and external disturbances simultaneously. To improve the estimation accuracy, the observer gains were adjusted using an adaptation law. To obtain a more comprehensive mathematical analysis and an accurate model for the ESO and to increase the degree of freedom, a Takagi–Sugeno fuzzy system was employed. The proposed AFESO relaxes the limitations of the ESO and improves the system performance as compared with the classical methods in the presence of time-varying disturbances. Next, a command-filtered backstepping controller is designed based on the barrier Lyapunov function method, which guarantees fast convergence of the tracking error as well as satisfying the output constraints of the system. The stability analysis showed that both the estimation error of the AFESO and the tracking error of the controller are bounded, and the tracking error converges to a small neighborhood of the origin. A simulating example of a flexible-joint manipulator shows the effectiveness of the proposed method as compared with the recently proposed method in the literature.