This mixed-methods study examined emotional intelligence (EI) as a factor of a leader’s ability to adapt and tolerate stress while leading day-to-day activity of an organizational merger. Continuous exposure to merger activity can trigger feelings and actions that create personal and social challenges for leaders; thus, impacting merger performance. Although a merger may be stressful for all entities involved, leaders expressed different perceptions of merger stress and adaptability based on their identification with the larger or smaller merger partner. Without assessment and awareness of a leader’s psychological health, leaders may succumb to the pressures of the merger and the new organization will be at risk of merger failure. The Emotional Quotient Inventory (EQ-i 2.0) self-assessment was administered followed by semi-structured interviews to better understand the relationship between emotional intelligence scores and narratives of the merger experience. Regression analysis reported a statistically significant relationship between the total EI score and the stress management score which indicated that a higher overall EI score was predictive of a better stress management score. Correlation testing showed no relationship between interview responses about adaptability to merger stressors and scores reported for stress tolerance and flexibility on the EI assessment. Emotional intelligence scores in stress tolerance and flexibility did not consistently reflect the leaders’ description of their actual merger experience. Additionally, there was no statistical significance in EI scores reported for leaders from the larger blood center in relation to leaders from the smaller blood center partners.