There is a strong trend in the development of control systems for multi-rotor unmanned aerial vehicles (UAVs), where minimization of a control signal effort is conducted to extend the flight time. The aim of this article is to shed light on the problem of shaping control signals in terms of energy-optimal flights. The synthesis of a UAV autonomous control system with a brain emotional learning based intelligent controller (BELBIC) is presented. The BELBIC, based on information from the feedback loop of the reference signal tracking system, shows a high learning ability to develop an appropriate control action with low computational complexity. This extends the capabilities of commonly used fixed-value proportional−integral−derivative controllers in a simple but efficient manner. The problem of controller tuning is treated here as a problem of optimization of the cost function expressing control signal effort and maximum precision flight. The article introduces several techniques (bio-inspired metaheuristics) that allow for quick self-tuning of the controller parameters. The performance of the system is comprehensively analyzed based on results of the experiments conducted for the quadrotor model.