Successfully managing invasive plants in natural systems is extremely difficult. Recently however, progress has been made with an approach focused on changing ecosystem processes through the disturbance regime. We performed a large-scale (3 ha) full-factorial field experiment in densely invaded woodland in Hluhluwe-iMfolozi Park, a savanna reserve in South Africa, to study the effect of fire on the control of the pan-tropical invasive exotic shrub Chromolaena odorata in combination with the conventional method, i.e. manual clearing and herbicide application. We show how fire interacted with the conventional clearing of C. odorata and induced an intense canopy fire that caused a shift from woodland to grassland. After 2.5 years of monitoring, grasses were still dominant and re-invasion minimal. It is important to note that fire without prior clearing did not have the same effect and was not successful in reducing densities of C. odorata. An integrated control practice targeting the species with mechanical and chemical methods, while simultaneously targeting its habitat through fire, effectively controlled dense C. odorata thickets during the course of the experiment. However, this approach transformed regular surface fires into high-intensity canopy fires that are rare in savannas. We discuss how this altered fire regime may threaten native habitats, including fire-sensitive forest patches and riverine woodlands within the savanna mozaic. This is an important dilemma for managers that should not be overlooked and asks for long-term data on the impact of control programs on the native vegetation.