Self-grooming is an innate, naturalistic behavior found in a wide variety of organisms. The control of rodent grooming has been shown to be mediated by the dorsolateral striatum through lesion studies and in-vivo extracellular recordings. Yet, it is unclear how populations of neurons in the striatum encode grooming. We recorded single-unit extracellular activity from populations of neurons in freely moving mice and developed a semi-automated approach to detect self-grooming events from 117 hours of simultaneous multi-camera video recordings of mouse behavior. We first characterized the grooming transition-aligned response profiles of striatal projection neuron and fast spiking interneuron single units. We identified striatal ensembles whose units were more strongly correlated during grooming than during the entire session. These ensembles display varied grooming responses, including transient changes around grooming transitions or sustained changes in activity throughout the duration of grooming. Neural trajectories computed from the identified ensembles retain the grooming related dynamics present in trajectories computed from all units in the session. These results elaborate striatal function in rodent self-grooming and demonstrate that striatal grooming-related activity is organized within functional ensembles, improving our understanding of how the striatum guides action selection in a naturalistic behavior.