Previous neuroscientific research revealed insights into the brain networks supporting goal-directed and habitual behavior, respectively. However, it remains unclear how these contribute to inter-individual differences in habit strength which is relevant for understanding not only normal behavior but also more severe dysregulations between these types of action control, such as in addiction. In the present fMRI study, we trained subjects on approach and avoidance behavior for an extended period of time before testing the habit strength of the acquired stimulus-response associations. We found that stronger habits were associated with a stronger decrease in inferior parietal lobule activity for approach and avoidance behavior and weaker vmPFC activity at the end of training for avoidance behavior, areas associated with the anticipation of outcome identity and value. VmPFC in particular showed markedly different activity dynamics during the training of approach and avoidance behavior. Furthermore, while ongoing training was accompanied by increasing functional connectivity between posterior putamen and premotor cortex, consistent with previous assumptions about the neural basis of increasing habitualization, this was not predictive of later habit strength. Together, our findings suggest that inter-individual differences in habitual behavior are driven by differences in the persistent involvement of brain areas supporting goal-directed behavior during training.