Nacional

Nacional reached the first division for the first time ever with a three-season spell from 1988. Under manager José Peseiro, the team returned for 2002–03 after winning promotion in third place. The team finished comfortably in 11th, with results including a 1–0 home win over S.L. Benfica on 28 September 2002 and a 3–2 win at C.S. Marítimo in the Madeira derby the following 2 February. Peseiro's successor Casemiro Mior took the team to a joint-best 4th place in 2003–04, including another home win over Benfica, shortly after that team had knocked them out of the quarter-finals of the Taça de Portugal. Stars of this team included Brazilians Paulo Assunção (defensive midfielder) and forward Adriano (16 and 19 goals in respective seasons), both of whom later played for FC Porto.

Nacional's debut European season in the 2004–05 UEFA Cup ended in the first round with a 4–1 aggregate loss to Spain's Sevilla FC. In January 2005, Mior left for Club Athletico Paranaense in his homeland. Manuel Machado led the team to fifth in 2005–06, again reaching the UEFA Cup, but left due to his wife and children living in continental Portugal. The club's second run in European competition again ended at the first hurdle, 3–1 on aggregate to CS Rapid București of Romania.

Under the returning Machado in 2008–09, again edged S.C. Braga for fourth spot. Brazilian forward Nenê earned the Bola da Prata for top scorer with 20 goals, three more than Benfica's Óscar Cardozo and Sporting CP's Liédson. The side also reached the last-four in the Portuguese Cup, losing on aggregate 5–4 to F.C. Paços de Ferreira, with the decider coming at the Estádio da Madeira in the 90th minute.

Nacional started the 2009–10 season without Nenê, who was sold in June to Cagliari Calcio of the Italian Serie A for a fee potentially rising to €10 million. However, in August the club won a European tie for the first time, defeating 2008 champions FC Zenit Saint Petersburg 5–4 on aggregate in the playoffs of the renamed UEFA Europa League; the team were heading out on the away goals rule until a last-minute goal from youngster Rúben Micael earned a 1–1 draw in Russia. Nacional were eliminated in the group stage, third behind SV Werder Bremen and Athletic Bilbao but ahead of FK Austria Wien. In 2010–11, former club players Predrag Jokanović and Ivo Vieira led the team to 6th and a European return, as well as the semi-finals of the Taça da Liga for the first time (at Porto's expense), losing 4–3 to Paços de Ferreira. In the following season, following Europa League playoff elimination by Birmingham City, the team made the national cup semi-finals again, losing 5–3 on aggregate to Sporting.

In his fourth of five spells as Nacional manager, Machado led the team to 5th in 2013–14, making the Europa League playoffs and falling at the first hurdle 5–2 on aggregate to FC Dinamo Minsk of Belarus. In the 2014–15 Taça de Portugal they made a third semi-final in seven years, again losing to Sporting. The 2016–17 season, which included Jokanović's fourth spell as manager, ended with relegation in last place, a conclusion to 15 years in the top flight.

Former Portugal international Costinha was hired in 2017 and won promotion at the first attempt as champions of the 2017–18 LigaPro; Cape Verde international striker Ricardo Gomes was the league's top scorer with 22 goals in 36 games and left the club for FK Partizan in Serbia at the end of his contract. Costinha left after relegation from the 2018–19 Primeira Liga, in which results included a 10–0 loss to eventual winners Benfica.

The 2019–20 LigaPro was abandoned due to the COVID-19 pandemic in Portugal, resulting in promotion for first-placed Nacional; it was the sixth promotion in the career of 34-year-old manager Luís Freire. The team were immediately relegated in last place, with Freire sacked in March 2021 and Machado seeing out the season in his fifth spell. The team reached the semi-finals of the 2022–23 Taça de Portugal, losing 7–2 on aggregate to Braga, while the league season went to the final day; a 3–2 home win over Académico de Viseu F.C. after losing at half time saved the team in 14th place while B-SAD took the relegation playoff position.