In a recent study, we used the dynamic temporal prediction (DTP) task to demonstrate that the capability to implicitly adapt motor control as a function of task demand is grounded in at least three dissociable neurofunctional mechanisms: expectancy implementation, expectancy violation and response implementation, which are supported by as many distinct cortical networks. In this study, we further investigated if this ability can be predicted by the individual brain’s functional organization at rest. To this purpose, we recorded resting-state, high-density electroencephalography (HD-EEG) in healthy volunteers before performing the DTP task. This allowed us to obtain source-reconstructed cortical activity and compute whole-brain resting state functional connectivity at the source level. We then extracted phase locking values from the parceled cortex based on the Destrieux atlas to estimate individual functional connectivity at rest in the three task-related networks. Furthermore, we applied a machine-learning approach (i.e., support vector regression) and were able to predict both behavioral (response speed and accuracy adaptation) and neural (ERP modulation) task-dependent outcome. Finally, by exploiting graph theory nodal measures (i.e., degree, strength, local efficiency and clustering coefficient), we characterized the contribution of each node to the task-related neural and behavioral effects. These results show that the brain’s intrinsic functional organization can be potentially used as a predictor of the system capability to adjust motor control in a flexible and implicit way. Additionally, our findings support the theoretical framework in which cognitive control is conceived as an emergent property rooted in bottom-up associative learning processes.