His career at Boro got off on the wrong foot when he was forced to limp off with a calf injury five minutes into his debut at Charlton Athletic. Whilst at Middlesbrough, Ehiogu quickly became a mainstay in the central defence since joining the club and rejoining his former teammate Gareth Southgate in central defence. He missed the start of the 2003–04 season with a knee injury sustained in the final match of the previous season. He returned in time to play in Boro's League Cup final win against Bolton Wanderers, the first major trophy in the club's history. Only into the third game at the start of 2004–05 season Ehiogu had an accidental clash with his own keeper Mark Schwarzer which resulted in knee ligament damage. Again he was forced to miss many important games, although Boro still managed to secure a place in the UEFA Cup for a second successive season.