Despite his bad results, he remained for the next season until a humiliating 3–1 defeat to Rio Ave lead Benfica's direction to sack him.

[7] In 1999, Manuel José signed with União de Leiria and left in April, to be replaced by José Mourinho, on his second year with seven games left to be played, while the team was on the run for their highest ever place, to sign with Egyptian giants, Al Ahly, with the main goal being to win the Egyptian Premier League.

Since returning to Al Ahly, Manuel José helped give the team a record-breaking unbeaten run of 55 matches.

Al-Ahly only conceded three defeats in 2006, with two of them coming in the CAF Champions League and the other in the FIFA Club World Cup, in the first half of the 2006–07 season, meaning the team went undefeated the whole 2005–06 season, these achievements enabled José to win the CAF Coach of the Year award in 2006, becoming the first non-African to win the award while managing a club.

Although reports were surfacing that he would be on the brink of taking over the Portugal national team after Luiz Felipe Scolari's departure, the Portuguese Football Federation hired instead Carlos Queiroz.

[13] After Angola's defeat, against Ghana, in the quarter-finals of the 2010 Africa Cup of Nations, he apologized the entire Angolan people for their premature elimination and left his post by mutual agreement.

[19] He had been pointed out as a coach likely to succeed Hassan Shehata after he left the Egyptian managerial position in early June 2011.

[22][23][24] Shortly after the clashes, Manuel José made a €47,000 donation to the Al-Ahly fund created to support the victims' families and attended the wake held in honour of the ones who had died, when he returned to Portugal he said he wanted to finish his career at the Egyptian club in remembrance of the lost souls.

He had held a press conference after the match stating that Al-Ahly department is trying to renew his contract but, he had refused as there is political unrest in Egypt and also for the stoppage of Football in the nation as he stated "Politics had corrupted football in Egypt" He is recognized as a football legend in Egypt by The Ultras fans either Zamlkawy or Ahlawy[27] On 3 July 2012, Manuel José was named as Persepolis's head coach and signed a one-year contract with the club, replacing Mustafa Denizli, who resigned from his position in June 2012 for personal reasons.