Assisted and automated ship maneuvering can contribute to safer and cleaner port operations. Power consumption can be reduced by optimizing the thrust allocation to the available actuators. Within the established structure for guidance, navigation and control, thrust allocation belongs to the control module. Each controller mode requires an associated allocation that distributes the commanded forces at the controller output to the ship’s actuators so that the desired motion is achieved. The allocation problem is formulated as a quadratic program. The paper focuses on a generic allocation approach for a vessel with a maximum of six actuator units. The method is explained using the specifications of the 52 m long research vessel DENEB and for the various phases of automatic port maneuvers in the area of German Naval Base Command Rostock-Warnemünde. The paper presents the results for dynamic positioning maneuvers with the real vessel under the influence of wind using the developed allocation approach.