In his last two years, a string of injuries (including one which caused him to miss the 2006 UEFA Cup Final) and long spells of regaining match fitness relegated Mendieta to the substitutes bench. He fell out of favour with manager Gareth Southgate, who made it clear that the player no longer featured in his first team plans. Reports suggested that Real Sociedad, Athletic Bilbao and Málaga CF were interested in purchasing the midfielder in the January 2007 transfer window, however no concrete agreement was ever made, and the transfer deadline passed amid speculation that the player was set for a move to Los Angeles Galaxy; towards its end, he was quoted to have said that he would fight for his place at Middlesbrough. A day later, "Boro's" chief executive Keith Lamb disregarded his comments saying that there was "no chance" of him featuring in the first team. He played his last game on 26 December 2006, against Everton.