Intensive practice of a new complex motor skill results in progressive improvement of performance. This induces neuroplastic changes, reflecting the transition from attention-demanding to more automatic performance throughout the learning. In the present fMRI study, learning-related cerebral activation changes during the acquisition of a new complex bimanual coordination pattern were examined, i.e., the 90 degrees out-of-phase pattern (90Phi). Furthermore, we investigated whether practice of this new pattern influenced the neural correlates associated with performance of a preferred intrinsic pattern. Twelve young healthy subjects were intensively trained on the 90Phi task, and underwent two fMRI scanning sessions in early (PRE) and late (POST) learning. Scanning sessions included performance of the trained 90Phi pattern, as well as the nontrained intrinsic in-phase pattern (InPhi). Kinematics registered during training and scanning experiments showed that the new 90Phi pattern was acquired successfully, resulting in learning-related brain activation changes. Activation decreases were observed in the right prefrontal cortex (DLPFC and dorsal premotor), in the right middle temporal and occipital cortices and in the posterior cerebellum. Conversely, increases were found in the basal ganglia and hippocampus. Interestingly, activity elicited by the InPhi task also evidenced within-subjects PRE/POST differences (although kinematics InPhi performance was equivalent in both sessions). In particular, the learning-related decreases found for the 90Phi pattern in the cerebellum, the occipital and temporal gyri were similarly observed for the intrinsic InPhi pattern. Moreover, InPhi performance induced PRE/POST increases of activity in the left superior frontal gyrus. Our fMRI results suggest that intensive practice of a new complex coordination pattern impacted, at least temporarily, on the neural correlates of preferred intrinsic coordination patterns. Additional neural recruitment might reflect increased mental effort to prevent negative transfer from the learned mode onto the intrinsic coordination mode.