Cognitive Control (CC) plays an important role in learning and self-regulatory processes. Socioeconomic status (SES) has been linked to neural activity related to CC processing. Little is known about the influence of cognitive interventions on children’s brain functioning, and how the individual differences modulate the impact of those interventions. In the present study, a quasi-experimental design was implemented to evaluate the impact of cognitive training on cognitive performance and neural activity in 85 preschoolers from low-SES homes. Before and after the intervention children were assessed with a mobile EEG device during the performance on a Go/NoGo task. Based on their performance on a Stroop-like task at the pre-intervention stage children were classified into two groups (high- and low-performers) and then assigned to intervention and control groups within each performance level. Each group completed a set of activities during the intervention stage with different difficulty levels based on their basal performance. Results showed that children in the high-performance intervention group benefited the most at the neural level (i.e., conflict-related activity). The low-performance intervention group also verified changes at the behavioral level (i.e., increased RT´s after error/go ratio). Findings contribute to the consideration of individual differences in the design of interventions with adaptive algorithms, and the use of neural technology in ecological contexts.