His professional career was mainly associated with Racing de Santander – he also represented Real Madrid for two years – and he played 447 La Liga matches over 17 seasons, scoring 43 goals.

[3] After a loan to Badajoz (Segunda División)[3] and scoring 14 goals in 72 league games with Racing from 1998 to 2000,[1] Munitis attracted attention from La Liga giants Real Madrid, who signed him for £6.8 million.

[6][7] In the following off-season, he was purchased up by Deportivo de La Coruña on a free transfer;[8] after a poor first year he would be one of the Galicia side's most important attacking players, also being used as a left winger in order to provide rest for veteran captain Fran and being his replacement when he retired at the end of 2004–05.

[9] Munitis returned to Racing in July 2006, forming an interesting attacking partnership with gigantic Serbian Nikola Žigić in his debut campaign[10][11] and helping it achieve a first ever qualification for the UEFA Cup in his second.

[13][14] In 2009–10, the 34-year-old Munitis was again an undisputed starter, but did not manage to find the net in 29 appearances, and his season was over during a 3–1 home victory over Espanyol due to a knee injury, on 14 April 2010;[15] at that time he ranked second in assists, only trailing Barcelona's Lionel Messi.

In the following campaign he failed to score in 32 matches, and Racing returned to the second tier after one decade, with the player announcing shortly after his decision to leave his main club.

[21] Described as a "poacher" in the media, Munitis was capable of playing either as a forward or midfielder but was usually deployed as a left winger, and was one of the shortest players in the Spanish top flight throughout his career.