In 2000, it reached the second division for only the second time, being relegated at the end of the season, but immediately gaining promotion back.

In 2004–05, it achieved its best ever classification in the category, finishing in fourth position, nine points behind last promotee C.F.

In the following campaign, the club ended its Portuguese Cup run with a valiant display against eventual winners FC Porto, losing 0–1 away.

On 27 September 2007, with Marco already in division three, the Portuguese Football Federation punished the club with relegation, suspension from all activity during two years and a €2,500 fine, following failure to appear in four league games.

= Tier; 1 = Portuguese League; 2 = Liga de Honra; 3 = Segunda Divisão / Campeonato Nacional de Seniores 4 = Terceira Divisão; 5 = AF Porto First Division Pos.