Coaching career
Muñoz started working as a manager in the mid-1990s, being successively at the helm of RCD Mallorca, CD Logroñés, UE Lleida, Villarreal CF and Zaragoza. With the last of those teams, he won the 2003–04 domestic cup with a 3–2 extra time victory over Real Madrid's Galácticos.
On 8 October 2006, Muñoz signed a two-year contract with Greece's Panathinaikos FC, becoming their 18th coach in ten years. However, he returned to Spain in June 2007 to take over at Recreativo de Huelva, from where he was sacked the following February.
For the 2008–09 campaign, Muñoz was appointed at Getafe CF. Following a string of seven losses in nine games that left the team from the outskirts of Madrid one point above the relegation zone, he was dismissed in April 2009, making way for former Real Madrid player Míchel.
In late December 2010, after more than one year out of football, Muñoz was named head coach of Russian Premier League side FC Terek Grozny. He left his post in Chechnya after less than one month due to failed contract negotiations, being replaced by Ruud Gullit.
Muñoz returned to active in early September 2011, when he became Neuchâtel Xamax FCS's third manager of the season, replacing his compatriot Joaquín Caparrós. He continued his career in the Swiss Super League, with a brief stint at FC Sion from December 2012 until the following February.
On 19 March 2014, Muñoz returned to Zaragoza, succeeding Paco Herrera at a club at risk of relegation to Segunda División B. He was dismissed on 24 November with the side in 8th, one point off the play-offs.
