Electroencephalographic (EEG) microstates are brain states with quasi-stable scalp topography. Whether such states extend to the body level, that is, the peripheral autonomic nerves, remains unknown. We hypothesized that microstates extend at the brain-heart axis level as a functional state of the central autonomic network. Thus, we combined the EEG and heartbeat dynamics series to estimate the directional information transfer originating in the cortex targeting the sympathovagal and parasympathetic activity oscillations and vice versa for the afferent functional direction. Data were from two groups of participants: 36 healthy volunteers who were subjected to cognitive workload induced by mental arithmetic, and 26 participants who underwent physical stress induced by a cold pressure test. All participants were healthy at the time of the study. Based on statistical testing and goodness-of-fit evaluations, we demonstrated the existence of microstates of the functional brain-heart axis, with emphasis on the cerebral cortex, since the microstates are derived from EEG. Such nervous-system microstates are spatio-temporal quasi-stable states that exclusively refer to the efferent brain-to-heart direction. We demonstrated brain-heart microstates that could be associated with specific experimental conditions as well as brain-heart microstates that are non-specific to tasks.