Church has served as acting department secretary since January when Alvin Dominguez retired from the top administrator post.
Martinez announced Church's appointment on Friday. He is subject to confirmation by the state Senate.
Church has worked for the department for 20 years, including as chief of staff and deputy secretary of business and financial operations. As part of his duties, Church has managed agency offices dealing with legal affairs, accounting, budgets, audits, human resources and information technology.
Church graduated from high school in Roswell and from the University of Northern Colorado.