Here we test the hypothesis that frequency and topographically specific changes in the strength of functional cortico-cortical coupling occur during the acquisition of a completely new task. To this end we studied the behavioural and cortical dynamics of a bimanual multifrequency coordination pattern during which one hand moved at twice the frequency of the other hand. This pattern represents a noninherent assignment and necessitates training before appropriate interlimb decoupling takes place. Results showed that acquisition of the multifrequency task was associated with an improved behavioural output that matched specific changes in the electroencephalogram dynamics. In particular, practice of the coordination pattern was accompanied by a decrease in coherence between the primary sensorimotor regions, and over the midline area in the alpha and beta bands, respectively, along with an increase in functional interhemispheric coupling between the prefrontal areas in the gamma band. These data suggest that the strength of cortico-cortical connectivity is adaptively modified across regions and across frequencies during early learning as the functional couplings are created and optimized for the purpose of movement execution.