BACKGROUND: Helicopter pilots are involved in a complex multitask activity, implying overuse of cognitive resources, which may result in piloting task impairment or in decision-making failure. Studies usually investigate this phenomenon in well-controlled, poorly ecological situations by focusing on the correlation between physiological values and either cognitive workload or emotional state. This study aimed at jointly exploring workload induced by a realistic simulated helicopter flight mission and emotional state, as well as physiological markers. METHOD: The experiment took place in the helicopter full flight dynamic simulator. Six participants had to fly on two missions. Workload level, skin conductance, RMS-EMG, and emotional state were assessed. RESULTS: Joint analysis of psychological and physiological parameters associated with workload estimation revealed particular dynamics in each of three profiles. 1) Expert pilots showed a slight increase of measured physiological parameters associated with the increase in difficulty level. Workload estimates never reached the highest level and the emotional state for this profile only referred to positive emotions with low emotional intensity. 2) Non-Expert pilots showed increasing physiological values as the perceived workload increased. However, their emotional state referred to either positive or negative emotions, with a greater variability in emotional intensity. 3) Intermediate pilots were similar to Expert pilots regarding emotional states and similar to Non-Expert pilots regarding physiological patterns. DISCUSSION: Overall, high interindividual variability of these results highlight the complex link between physiological and psychological parameters with workload, and question whether physiology alone could predict a pilot's inability to make the right decision at the right time.