This project concerns development of a proof of concept self-tuning system for a Mission OS (TM) boiler system. Furthermore, a method to ensure clean combustion, in case of fuel actuator saturation, has been developed. The Mission OS (TM) boiler system is modelled as three separate non-linear models; a model of the Mission OS (TM) boiler, the feed water actuator system and the fuel actuator system. For design of SISO controllers, the complex non-linear models are simplified to integrator models. Both the complex non-linear models and the simple integrator models are verified using measurement data from the boiler system. Controllers are designed to comply with the developed self-tuning scheme, capable of identifying model parameters during the start-up phase of the boiler system. The identified parameters includes fuel actuator servo characteristics, feed water valve characteristics, a curveband, describing the oil/air ratio, used as oxygen level control and pressure build-up characteristics. Based on these parameters, controller parameters are calculated prior to operating the boiler. Control of the fuel actuator system for the Mission OS (TM) boiler system includes Pulse Width Modulation (PWM) position control of oil valve and air damper. To comply with the curveband, in case of PWM saturation, a constrained minimisation problem has been derived and solved by a model predictive reference correction scheme, ensuring steady oxygen level by compliance of the curveband. Finally, to assess potential improvements of the water level control, a Kalman estimator is designed to estimate the mean water level and the unmeasurable steam consumption. The developed methods are verified by simulation and shows satisfactory performance.