• Assess how the processing of emotional information affects cognitive control processes in BP and SZ. • Inhibiting irrelevant emotional stimuli during a cognitive task proved difficult in both the SZ and BP groups. • The BP group had longer RTs for the negative emotional valence. • SZ group had difficulty inhibiting irrelevant stimuli in the emotional Stroop task, indicating impaired inhibitory control. Bipolar disorder (BP) and schizophrenia (SZ) are both psychiatric conditions characterized by deficits in cognitive control (executive function and attention) and emotion regulation. The emotional Stroop task makes it possible to measure such deficits and to study the impact of emotions on cognitive control. The objective of the present study was thus to explore this impact in people with BP or SZ. Participants were 21 individuals with BP, 23 participants with SZ, and 42 control participants (HC). Participants with SZ had greater cognitive impairments than participants with BP, who had greater cognitive impairments than HC. The BP group had longer reaction times than the HC group for the negative valence, and the SZ group had longer reaction times than the HC group for all three valences (i.e., positive, negative, and neutral). We did not observe an effect of emotional valence within any of the three groups. The SZ and BP groups had difficulty inhibiting irrelevant emotional stimuli during a cognitive task, reflecting deficits in the engagement of cognitive control during emotion regulation in both pathologies.