[8] Returned to Porto, Conceição's runs down the right flank, combined with a good scoring record, helped them to back-to-back national championships and a Taça de Portugal triumph.

[16] His side reached the cup final, which they lost to Fiorentina 2–1 on aggregate with his campaign ending through injury in the first leg; he was subsequently linked to Manchester United, Juventus and Milan.

[21] He was ineligible for their UEFA Champions League triumph having already represented Lazio in that year's competition,[20] but scored his only goal of his second spell from the penalty spot on his debut on 21 January in a 4–0 win at the Estádio das Antas in the last 16 of the national cup,[22] eventually losing the final to Benfica.

[29] His unlikely signing was largely attributed to club director of football Zisis Vryzas, and the presence of Portuguese manager Fernando Santos on the bench; though he initially struggled even to return to proper fitness levels, he was instantly given the number No.

Conceição played 56 times with the Portugal national team and scored 12 goals,[31] his debut being on 9 November 1996 in a 1–0 home win over Ukraine for the 1998 FIFA World Cup qualifiers.

[32] Early in his international career, Conceição was not known for his scoring prowess but, at UEFA Euro 2000, Portugal reached the semi-finals with a major contribution from him: in the third and final match of the group stage, against defending champions Germany in Rotterdam, he netted a hat-trick for all of the game's goals;[33] the national side had guaranteed first place in the first two rounds, so it played mostly with substitutes, but he cemented his place in the starting XI for the rest of the tournament and subsequent call-ups.

In qualifying for the 2002 World Cup, Conceição scored four goals as Portugal finished top in a group that also featured the Republic of Ireland and the Netherlands (netting against both).

[34][35] On 13 October 2009, Conceição announced his decision to retire as a professional footballer, and to continue working at PAOK as technical director,[36][37] accepting Vryzas' proposal for the seat left vacant when he assumed presidency early on.

On 30 May 2010, a few weeks after Santos' resignation as manager, he left the Thessaloniki club[38] and rejoined another former team, as part of Standard Liège's coaching staff led by Dominique D'Onofrio.

[49] Conceição signed a two-year contract with Braga on 26 May 2014;[50] the team had just finished the campaign one place below Académica with the same number of points, resulting in the first time in ten years that the club was out of European competitions.

[53] Following this defeat, president António Salvador released an official statement that angered Conceição, resulting in a "violent discussion" between the two and leading to the latter's sacking.

[58][59] Conceição was named manager of Ligue 1 club Nantes on 8 December 2016, replacing the dismissed René Girard at a side second from bottom.

[63] In February 2017, Conceição was linked to the vacant managerial position at struggling Premier League title holders Leicester City, but Nantes chairman Waldemar Kita insisted he would see out his two-year contract.

[64] It was announced on 6 June that he had quit his position and accepted a proposal from Porto,[65] citing personal reasons, including the possibility to live close to his family in Portugal.

[78] His third league title was sealed on 7 May, with a last-minute winner by Zaidu Sanusi at Benfica,[79] and 15 days later a 3–1 defeat of Tondela decided the domestic cup final.

[82] On 4 June, his team won the 2023 Taça de Portugal final 2–0 against Braga, making him the first manager to win that honour three times with Porto; his ten trophies made him the second most successful in Portuguese football, after Jorge Jesus' 12.

[86] On 30 December 2024, Conceição returned to the Italian top tier with AC Milan;[87] he replaced his compatriot Paulo Fonseca, who had been dismissed the day before.

[89] In the final on 6 January, in which the Rossoneri started no national players for the first time in the history of the Derby della Madonnina, having done likewise in the previous match,[90] his team came from behind 2–0 to beat Inter 3–2 and claim the title,[91] and he became in the process their fastest manager to do so by breaking Vincenzo Montella's 2016 record of 18 games.

He occasionally deployed a 4–4–2 formation;[97] Fabio Capello commented on this approach saying: 'As a coach he has done very, very well at Porto, demonstrating great tactical and attacking attention.