Abstract— This article discusses the development of a new control strategy that merges an ultra-local model control with an auto-tuning PID control applied to a flexible mechanism with an endpoint load. This will help obtain a suitable control system to well manage the behavior of this flexible structure. The proposed approach uses an ultra-local model control, which consists of locally modeling such a system that is instantly updated only from the knowledge of the input and output system then estimating its parameter via an algebraic derivation approach. And then of auto-tuning PID control which consists on automatically tuning the PID controller's gains using the pole placement technique. In order to evaluate the robustness and efficiency of the proposed approach against the internal vibration of the flexible structure and to the external distribution, the new control has been applied to a flexible manipulator robot using several motion profiles. Results are presented and discussed which illustrate the validity of the proposed control strategy that has been carried out in the presence of internal vibration and several inputs.