Results improved following a European win against Lille, with Benfica climbing several places and defeating Porto in the Clássico.

This success was not replicated domestically; in mid-March, Benfica lost further ground in the Primeira Liga and were eliminated from the Portuguese Cup.

Koeman's side recovered, but they were eliminated by Barcelona from the Champions League and failed to overtake Sporting when they dropped seven points in three match-days.

After leading Benica to their first league title in ten seasons, Giovanni Trapattoni departed the club for personal reasons.

[10] Vital to his new formation, Koeman asked for more wingers, such as Andy van der Meyde,[11] and Boudewijn Zenden,[12][13] but Benfica did not sign them.

[14][15][16] To improve Koeman's options up-front, composed of Nuno Gomes and Mantorras, Benfica tried but failed to sign Jon Dahl Tomasson.

[23] The pre-season began on 4 July 2005 with medical exams,[24] followed by the first training session on the next day, with two thousand supporters present at the Estádio da Luz.

[27][28] Back in Portugal, Benfica faced two Premier League opponents, losing to Chelsea,[29] and defeating West Bromwich.

[30] Afterwards, Benfica played three Portuguese teams, winning against Barreirense and Estoril Praia,[31][32] and drawing with Vitória de Guimarães.

[35] On the 13 August, Benfica faced Vitória de Setúbal at the Estádio Algarve, winning 1–0 with a goal from Nuno Gomes.

[39] On 26 August, Benfica took part in the draw for the group stage of the 2005–06 UEFA Champions League; their first in the new century because they failed to qualify in the past two seasons.

[47] With two losses and a draw in three match-days, Koeman broke a club record for the worst season start in history, already eight points from the top of the league.

[51] On 18 September, Benfica hosted União de Leiria; Koeman reverted to the 4–2–3–1 formation that Giovanni Trapattoni regularly used.

Simão put Benfica back in front with a deflected shot that beat Márcio Paiva, ensuring a third consecutive win that reduced the distance to the league leader to four points.

[61] The draw allowed Benfica to remain in second place in Group D; Koeman was confident he could beat the Spaniards at home.

They were unable to beat Belenenses' keeper, dropping two points in a 0–0 draw and extending their winless run to six matches, the longest dry spell since 2001–02.

They struggled to beat Vitória de Setúbal's goalkeeper Marcelo Moretto throughout the game, only securing the win in the 90th minute through Nuno Gomes.

[96] Entering the decisive part of the season, and still present in all competitions, Benfica's first game of February was a visit to Estádio Dr. Magalhães Pessoa to face União de Leiria.

[97][98] On 8 February, Benfica met Nacional at home for the sixth round of the Portuguese Cup; the match ended in a goalless draw, even after extra time.

Geovanni opened the scoring in the first half, after which Nuno Gomes, Simão and an own goal from Roberto set the final result.

[101] The loss severely hampered their title defence after being overtaken by Sporting and Braga and allowing leaders Porto—their next league opponent—to gain an eight-point advantage.

According to Adrian Harte, the match was "largely disappointing", but Benfica secured a vital win against Liverpool when Luisão scored with an 84th-minute header.

[119] In April, Benfica were still battling for a Champions League semi-final spot while chasing Porto and Sporting in the domestic title race.

[120] Assistant manager Bruins Slot said, "The win allows us to keep pressure on our opponents and give us morale for Barcelona".

[124] Nonetheless, the draw granted Porto the chance to increase their lead to nine points with four games left, making the title renewal "impossible," as Koeman described it.

Hoping to take advantage of Sporting's slip hours earlier and only battling for a direct qualification for the next Champions League campaign, Benfica beat the home side 2–0, with goals from Tiago and Mantorras.

Benfica led the game most of time, but conceded a late goal from Ricardo Fernandes and lost the chance to overtake Sporting.

[129] The win meant Koeman had surpass Giovanni Trapattoni's previous points total (67–65), but without the same glory; Porto had already won the league and Sporting was in good position to finish second.

[134] Koeman thanked Luís Filipe Vieira and José Veiga for their support in face of repeated criticism, and said, "This is very big club, but you cannot win all the time, although I admit, that in the Primeira Liga, he did not do everything he could.

Note 2: Players with squad numbers marked ‡ joined the club during the 2005-2006 season via transfer, with more details in the following section.