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Mindfulness-based cognitive therapy (MBCT), a meditation-based maintenance therapy, reduces the relapse risk in individuals suffering from major depressive disorder (MDD). However, only a few studies investigated the psychophysiological mechanisms underlying this protective effect. We examined effects of MBCT on trait rumination and mindfulness, as indicators of global cognitive style, as well as on residual depressive symptoms in a group of recurrently depressed patients (n = 78) in remission. Additionally, alpha asymmetry in resting-state electroencephalogram (EEG) was assessed. Alpha asymmetry has been found to be predictive of affective style and a pattern indicative of stronger relative right-hemispheric anterior cortical activity may represent a trait marker for the vulnerability to develop MDD. In line with previous findings, residual depressive symptoms and trait rumination decreased, whereas trait mindfulness increased following MBCT, while no such changes took place in a wait-list control group. Mean values of alpha asymmetry, on the other hand, remained unaffected by training, and shifted systematically toward a pattern indicative of stronger relative right-hemispheric anterior cortical activity in the whole sample. These findings provide further support for the protective effect of MBCT. In the examined patients who were at an extremely high risk for relapse, however, this effect did not manifest itself on a neurophysiological level in terms of alpha asymmetry, where a shift, putatively indicative of increased vulnerability, was observed.