Emotional processing in bipolar disorder (BD) is impaired. We aimed to measure the effects of mindfulness based cognitive-behavioral therapy (MBCT) in BD on emotional processing, as measured by event related potentials (ERP) and by heart rate variability (HRV). ERP and HRV were recorded during the completion of a visual matching task, which included object matching, affect matching, and affect labeling. Individuals with BD (n = 12) were compared with controls (n = 9) to obtain baseline data prior to the individuals with BD undergoing an 8-week MBCT intervention. ERP and HRV recording was repeated after the MBCT intervention in BD. Participants with BD had exaggerated ERP N170 amplitude and increased HRV HF peak compared to controls, particularly during the affect matching condition. After an 8-week MBCT intervention, participants with BD showed attenuation of ERP N170 amplitude and reduced HRV HF peak. Our findings support findings from the literature emphasizing that emotional processing in BD is altered, and suggesting that MBCT may improve emotional processing in BD.