Two phases of Transcendental Meditation (TM)—transcending and undirected mentation—were compared to each other and to task-free resting using multichannel EEG recorded from 20 TM practitioners. An EEG microstate analysis identified four classes of microstates which were labeled A, B, C and D, based on their similarity to previously published classes. For each class of microstates, mean duration, coverage and occurrence were computed. Resting and transcending differed from undirected mentation with decreased prominence of Class A and increased prominence of Class D microstates. In addition, transcending showed decreased prominence of Class C microstates compared to undirected mentation. Based on previous findings on the functional significance of the microstate classes, the results indicate an increased reference to reality and decreased visualization during resting and transcending compared to undirected mentation. Also, our results indicate decreased saliency of internally generated mentations during transcending compared to undirected mentation reflecting a more detached and less evaluative processing. It is proposed that the continuous cycling through these two phases of meditation during a TM session might facilitate and train the flexible modulation of the parameters of these microstates of these particular classes which are known to be altered in psychiatric disorders. This might promote beneficial stabilizing effects for the practitioner of TM.