Standard control laws have unique parameters that yield a certain response according to which model they are implemented on. Changes in the model will result in changes in the response, yielding the need for new ideal parameters. Adaptive controllers have the advantage of reducing the number of control parameters to be chosen by the pilot. Reducing this number of parameters can be beneficial, as obtaining the ideal parameters can become a time consuming process. Model reference adaptive control (MRAC) is the control approach that is considered in this paper. This approach has previously been implemented on a quadcopter by Achtelik [Adaptive Control oof a Quadcopter in the Presence of large/complete Parameter Uncertainties, 1, (2011)]. It is desired to implement the adaptive controller on the Pixhawk flight controller. The designed controller should integrate well with the existing PX4 firmware to allow users to still be able to use the flight controller as before. In order to integrate the adaptive controller with the PX4 firmware some modifications to the approach followed by Achtelik [1] is required. This paper focuses on the implementation of MRAC in PX4 firmware. This requires the use of rotation matrices as opposed to Euler angles. The mixer is also extracted from the adaptive law. From simulations it can be seen that rotation matrices show a significant improvement in reference tracking when it comes to simultaneous pitch, roll and yaw inputs. An autonomous mission was flown with the newly designed adaptive controller and also with the original PX4 controller. This showed successful integration of the adaptive controller with the existing firmware. An improvement in reference tracking for the adaptive controller, as opposed to the PX4 controller, was also found.