Abstract Adaptive input precompensators in conjunction with nonlinear controllers for multi-link flexible manipulators are considered in this paper. In an earlier paper, we had shown that application of a nonlinear inner-loop control reduces the variations in frequencies due to the geometrical configuration for multi-link flexible manipulators. This results in a better performance when input preshaping or any other controller based on a linear model is designed. To improve the performance of the system to parameter variations (e.g. changes in payload), an adaptive version of the advocated controller is utilized. This is achieved by estimating the time of application of the impulses for on-line preshaping and in the case of payload uncertainty, estimation of the payload and real-time adjustment of the nonlinear inner-loop based controller. Frequency domain Time-Varying Transfer Function Estimate (TTFE) and Empirical Transfer Function Estimate (ETFE) system identification algorithms are proposed for estimation of vibrational modes and unknown payload. Experimental results on a two-link flexible manipulator with adaptive nonlinear control and preshaping are provided to show the effectiveness of the advocated controllers. Overall, the present paper completely generalizes the adaptive input preshaping technique for multi-link flexible manipulators.