The Pompey Chimes

In 2004, after a recommendation, Jordan was brought into the coaching team at Portsmouth by manager Harry Redknapp to work alongside him and his assistant manager, Kevin Bond. Under Redknapp, Jordan went on to win the 2008 FA Cup Final with Portsmouth. They beat Cardiff city 1-0 at Wembley Stadium on 17 May.

While working as a coach under Redknapp at Portsmouth, Jordan said of his career and the possibility of future management roles, with clubs or Scotland, "I’m still ambitious and I’m desperate to do well here, along with the other people...I wouldn’t rule [management] out, but I’m not chasing it. I get on well with [Redknapp] and we hope that we can achieve something. I won’t go chasing every job that’s going, I know what I am and what I can do, but I’m not going down the route of applying for jobs."

Jordan continued to coach the team under the management of Velimir Zajec and Alain Perrin. He took over as caretaker manager for two games in November 2005 after Perrin's departure, before Redknapp returned after resigning from Southampton.

On the morning of 26 October 2008, after agreeing a compensation deal of £5m, Redknapp left Portsmouth to become the new manager of Tottenham Hotspur. This left assistant manager Tony Adams and first team coach Jordan to take charge of the team for the 1-1 home draw against Fulham the same day.

On the question of whether both would follow him, when he left Redknapp said he believed former Arsenal player Adams would not follow due to the Tottenham-Arsenal rivalry, but said "Joe Jordan has been fantastic for me and I would always be pleased to have him with me anywhere. But he is at Portsmouth at the moment and it is up to him and the club to see what will happen in the future."^[ On his appointment as the permanent Portsmouth manager two days later, Adams said he was keen to keep Jordan, stating “Joe is Portsmouth through and through, he's part of the woodwork, but he's a big man and will make his own decision.”

On 7 November 2008 Jordan left Portsmouth to join Redknapp at Tottenham Hotspur as first team coach, reforming the original Portsmouth back room team after Redknapp had also brought the recently sacked Bournemouth manager Kevin Bond as Tottenham assistant manager. Portsmouth praised Jordan's “significant contribution” on his departure after four years at the club.