[4] After graduating from law school, Muñiz clerked for Judge Thomas Aquinas Flannery of the United States District Court for the District of Columbia, from 1997 to 1998, and for Judge José A. Cabranes of the United States Court of Appeals for the Second Circuit, from 1998 to 1999.

He rejoined the Bush administration in April 2005 as general counsel of the Florida Department of Financial Services,[7] leaving that position in November 2006.

At that firm, he represented Florida State University against a lawsuit brought by a student who accused quarterback Jameis Winston of raping her.

[10] In March 2017, Muñiz was nominated by President Donald Trump to become the General Counsel of the United States Department of Education.

[2] He became a senior advisor in the Office of Secretary of the department in February 2018, and was confirmed as General Counsel by the U.S. Senate in April 2018, by a vote of 55–43.