Abstract: Prior work has linked meditation practice to improvements in interference control. However, the mechanisms underlying these improvements are relatively unknown. In the context of meditation training, improvements in interference control could result either from increases in controlled attention to goal-relevant stimuli, or from reductions in automatic capture by goal-irrelevant stimuli. Moreover, few studies have linked training-related changes in attention to physiological processes, such as inflammatory activity, that are thought to influence cognitive function. This study addresses these gaps by examining associations between cognitive performance and cytokines in the context of an intensive meditation retreat. Participants were randomly assigned to complete 3 months of meditation training first, or to serve as waitlist controls. The waitlist-control participants then later completed a separate 3-month training intervention. We assessed participants’ interference control with a flanker task and used computational modeling to derive component processes of controlled and automatic attention. We also collected blood samples at the beginning, middle, and end of training to quantify changes in cytokine activity. Participants who completed training evidenced better controlled attention than waitlist controls during the first retreat intervention, and controls showed significant improvements in controlled attention when they completed their own, second retreat. Importantly, inflammatory activity was inversely associated with controlled attention during both interventions. Our results suggest that practice of concentration meditation influences interference control by enhancing controlled attention to goal-relevant task elements, and that inflammatory activity relates to individual differences in controlled attention.