He bounced back with a good run with Vitória de Setúbal, and won the best Portuguese coach prize.

In August 2006, he was appointed manager of the Portugal under-21 national team, reaching positive results in the UEFA Championships.

In July 2008, Couceiro was then appointed the head coach of Kaunas, the Lithuanian A Lyga club controlled by Vladimir Romanov.

[2] In his first competitive match as manager, Lithuania defeated Romania 3–0 in Cluj-Napoca for a 2010 FIFA World Cup qualifier.

[3] On 26 February 2011, following the dismissal of Paulo Sérgio, Couceiro was named caretaker manager of Sporting CP for the remainder of the 2010–11 season.