A method for controlling friction stir welding is provided. The method may include initiating friction stir welding and determining the position of a friction stir welding tool and at least one part being welded. The method may also include adjusting the position of the friction stir welding tool while friction stir welding based at least in part on the positions of the tool and at least one of the parts. The position of the parts may be determined downstream of the friction stir welding tool in order to prospectively account for the position of the parts. Accordingly, the position of the friction stir welding tool may be dynamically adjusted during friction stir welding to account for part movement. Related systems and computer code are provided.