This study primarily tests whether incarceration negatively affects cognitive functioning; namely emotion regulation, cognitive control, and emotion recognition. As a secondary interest, we test protective effects of a Cognitive Behavioral Therapy/Mindfulness Training (CBT/MT) intervention. Dormitories containing 197 incarcerated males aged 16-18 were randomly assigned to either a CBT/MT program or an active control condition. A cognitive task was administered pre-treatment and again four months later, upon treatment completion. Performance on all outcome variables was significantly worse at follow-up compared to baseline. There were marginally significant group by time interactions. While the control group performance significantly declined in both cognitive control and emotion regulation, the CBT/MT group showed no significant decline in either outcome. This is the first study to probe the effects of incarceration on these three processes. Findings suggest that incarceration worsens a known risk factor for crime (cognitive functioning), and that a CBT/MT intervention may help buffer against declines.