Research on conflict adaptation suggests that complex networks are involved in the detection and resolution of conflicts. These networks are believed to be different depending on whether the conflict occurs in emotional or non-emotional contexts. In addition, the adaptation to both types of conflict also seems to have different neural bases. The main aim of the present study was to compare conflict adaptation in two clinical groups – patients with schizophrenia (SZ) and patients with borderline personality disorder (BPD) – and a healthy control group during emotional and non-emotional versions of a facial Stroop task. We considered that the neural impairment and neuropsychological profile of these populations would be interesting to examine the above-mentioned mechanisms. Results showed that the performance was worse with incongruent compared to congruent stimuli in both task contexts. The Stroop effect was more marked in both clinical groups and greater in the SZ group. By contrast, the Gratton effect was clearly present in the SZ group, but was inverted in the BPD group mainly in the emotional task. Specifically, participants with BDP had a higher error rate in the current incongruent trial when the previous trial was incongruent in the emotional task. These results suggest that SZ and BDP groups have different patterns of conflict adaptation. Results are discussed according to the clinical characteristics and neural systems affected in each of these psychopathological disorders.