While considered analogous to physical practice, the nature of imagery-based skill acquisition—specifically whether or not both effector independent and dependent encoding occurs through motor imagery—is not well understood. Here, motor imagery-based training was applied prior to or after physical practice-based training to probe the nature of imagery-based skill acquisition. Three groups of participants (N = 38) engaged in 10 days of training of a dart throwing task: 5 days of motor imagery prior to physical practice (MIP-PP), motor imagery following physical practice (PP-MIP), or physical practice only (PP-PP). Performance-related outcomes were assessed throughout. Brain activity was measured at three time points using fMRI (pre/mid/post-training; MIP-PP and PP-MIP groups). In contrast with physical practice, motor imagery led to changes in global versus specific aspects of the movement. Following 10 days of training, performance was greater when motor imagery preceded physical practice, although remained inferior to performance resulting from physical practice alone. Greater activation of regions that support effector dependent encoding was observed mid-, but not post-training for the PP-MIP group. Findings indicate that changes driven by motor imagery reflect effector independent encoding, providing new information regarding how motor imagery may be leveraged for skill acquisition.