The ability to sequence discrete movements in new ways enables rich and adaptive behavior. Such flexibility can be computationally costly and result in halting performances. Practicing the same motor sequence repeatedly, however, can render its execution precise, fast, and effortless, i.e., ‘automatic’. The basal ganglia are thought to underlie both flexible and automatic motor sequences, yet how their contributions differ across these modes is unclear. We parse this in rats trained to perform the same motor sequence in both modes, focusing on the sensorimotor striatum. Neural recordings revealed a kinematic code independent of execution mode. While lesions affected the detailed kinematics across modes, they disrupted high-level sequential structure for automatic but not visually-guided flexible behaviors. These results suggest that while the basal ganglia contribute to learned movement kinematics and are essential for ‘automatic’ motor skills, they can be dispensable for the flexible sequencing of discrete motor elements.