An automated crop production system for controlled environment agriculture that includes a horizontal-to-vertical grow tower interface between a vertical grow structure that includes vertical grow towers and associated conveyance mechanisms for moving the vertical grow towers through a controlled environment, and a processing system that performs one or more processing operations—such as harvesting, cleaning and/or transplanting—on the grow towers in a substantially horizontal orientation. The present disclosure also describes an automated crop production system for controlled environment agriculture that selectively routes grow towers through various processing stages of an automated crop production system.