Demand for fully autonomous VTOL aircraft with high agility has exposed the shortcomings of Euler‐angle models: limiting factors such as the presence of singularities and the need for expensive trigonometric operations impact the reliability and safety of autonomous systems and impair the execution of highly-aggressive manoeuvres. Quaternions offer a singularity‐free alternative, yet their use on full‐scale helicopters remains underexplored. Addressing this gap in research, this paper introduces a methodology for converting existing Euler‐based linear models of a Bo105 helicopter to quaternion form, preserving model fidelity. A hierarchical flight control system is then designed, controlling attitude with a novel implementation of Linear Quadratic Integral (LQI) control with quaternions, and commanding velocity and position using PI and P controllers. The controller is tuned using a structured approach implementing the Particle Swarm Optimization (PSO) algorithm. The system is then augmented with a Finite State Machine (FSM) autopilot to follow offline-generated trajectories. The implemented system was evaluated by simulating a slalom and a pop-up manoeuvre: the simulations demonstrated maximum tracking errors of 5 m for slalom and 7 m for pop‐up, primarily due to velocity‐loop delays, while achieving zero steady‐state error in the position. These results confirm the effectiveness of quaternion‐based modelling and control for agile, autonomous VTOL operations.