BACKGROUND: Mindfulness-based interventions (MBIs) are effective in treating major depression. Because mindfulness involves monitoring and accepting current experiences, it may lead people resolve incongruencies between emotional responses that would otherwise remain unnoticed. Mindfulness may thus foster congruence between implicit and explicit emotions. The current randomized controlled trial tested this notion. METHODS: N = 39 patients with an acute depressive episode were randomly assigned to an 8-week MBI (n = 24) or a psychopharmacological consultation condition (n = 15). Explicit and implicit mood and depressive symptoms were assessed before treatment and at the end of treatment. RESULTS: Compared with the control condition, patients receiving MBI demonstrated higher congruence between implicit and explicit negative mood after treatment. There was no such difference in congruence of implicit and explicit positive mood. Additional analyses showed that only within the MBI group, individual differences in explicit mood became less stable. In contrast, individual differences in implicit mood remained stable in both groups. LIMITATIONS: There was no control group including an active psychological intervention, the sample was small, and emotional congruence was not assessed within persons. CONCLUSIONS: These findings correspond with the idea that mindfulness reduces incongruencies between implicit and explicit emotional responses. We found preliminary evidence for this effect for negative emotional responses. There was suggestive evidence that congruence arose from the alignment of explicit responses (which became less stable) to implicit responses (which remained stable). Studying the interplay between implicit and explicit processes may shed light on the working mechanisms of clinical-psychological interventions.