Genetic factors are a well-established risk factor for children’s conduct problems. Specifically, the low activity variant of the Monoamine Oxidase-A (MAOA) gene is one of the most investigated. Most studies focused on MAOA’s interaction with environmental factors, while little is known about the possible interaction with psychological processes, such as affective decision-making (ADM). The current study is aimed to investigate whether MAOA variants, ADM skills, and their interaction are associated with higher levels of teacher-reported conduct problems in a sample of at-risk children. DNA was extracted from a sample of 157 at-risk children (mean age 10.24 years, range 9.17–11.79, 70% boys). ADM skills were assessed with the Iowa Gambling Task. Children’s conduct problems were measured with the Behavior Assessment System for Children-Teacher Rating Scales (BASC-TRS). Regression results showed that ADM skills significantly interacted with MAOA variants in predicting children’s conduct problems. Among children with the low activity MAOA variant, conduct problems were significantly higher in children with lower ADM. Results suggest that ADM may be a protective factor for children with the low activity variant and shield them from the genetic variant’s risks. Treatment implications are discussed.