Flight missions are highly dynamic and cognitively demanding multitasking situations. Navigating a helicopter or an aircraft safely requires sophisticated cockpit task management strategies. Multiple flight instruments have to be operated simultaneously in a goal-oriented manner despite various visual and auditory distractions. Task prioritization is one example of an effective task management strategy. For this, cognitive control is highly relevant, which is also subject to the stability-flexibility dilemma. The stability-flexibility dilemma of cognitive control relates to the contradictory demands of cognitive control to enable goal-directed behaviour. On the one hand, cognitive stability is necessary to shield goals from interference. On the other hand, cognitive flexibility enables flexible task switching. While the stability-flexibility dilemma has often been studied in simple stimulus-reaction experiments, its implications in more applied settings like flight missions were less researched. To address this, three experiments were conducted. The stability-flexibility dilemma was manipulated using a reinforcing mechanism in a virtual flight environment (MATB). Participants were instructed to prioritize either a tracking task (stable condition) or no tasks (flexible condition). The respective task prioritization strategy was reinforced via a scoring mechanism. Performance and eye-tracking results underscore the profound impact of task prioritization on dynamic multitasking scenarios. Future studies should also consider a qualitative assessment of the stability-flexibility dilemma, offering insights into how pilots navigate these challenges in different flight phases.