The monitoring of conflicting information, including emotional information, is essential for goal-directed acting. Even though the neurophysiological and functional neuroanatomical underpinnings of these processes have been investigated intensively, what has been examined at the neurophysiological level is still insufficient to explain/better understand the processes postulated as relevant by the cognitive theory of emotional conflicts. This particularly refers to how representations of emotionally conflicting information are handled in possibly different functional neuroanatomical structures and neural activity profiles. We investigated this question with an emotional Stroop task combining various EEG analysis methods in a sample of n = 44 healthy participants. The results revealed robust emotional conflict effects on the behavioral level. The neurophysiological data analysis revealed that distinct functional neuroanatomical structures play specific roles during the processing of representational content during emotional conflict monitoring. Starting in sensory cortices, representational content of emotional conflicts can be tracked through the insular cortex to the inferior and superior parietal cortex and medial frontal cortices. Each of these regions process representational content coded by spatially independent activity profiles. The findings show that emotional conflict monitoring reflects a dynamic interplay of multiple brain regions, each processing specific aspects of task-relevant representations.