"Hands Clean" delves into the lingering effects of a past, taboo relationship, reportedly a recollection of a sexual relationship the singer shared with a much older man when she was approximately 14 years old. The song features a shuffling, largely acoustic-rock framework, and the narrative voice alternates between the presumed viewpoint of the older man and the singer's own feelings. It explores how such experiences stay with a person, even years later, with the chorus representing the singer's feelings about the secret kept between them. At its heart, it plays like a quiet unveiling of a hidden history.