In semi-final, Al Ahly faced South American champions Internacional on 13 Dec 2006, and Flavio played a decent game, scoring the draw goal with a great header in the second half. However, Al-Ahly eventually lost the match 1–2.
After having a very unsuccessful first season with the team during which he scored only one goal in the league, and being jeered by fans at many times, most notably when he missed a penalty kick against rivals El Zamalek in the African Champions League, Flavio had a very successful second season in 2006–2007, seeing him top the goalscorers chart of the Egyptian Premier League with 17 goals, a single goal ahead of international Egyptian teammate Emad Moteab. He proved to be instrumental in Al Ahly's formation in the next years, scoring many vital goals in critical moments. Generally Flavio keeps an extremely low profile and rarely appears in the media or give any press statements. Such attitude is highly appreciated by his club administration, since it agrees with the club's policies.
In his last season with Al Ahly (2008–2009), Flavio managed to score Al Ahly's only goal during the Egyptian Premier League play-off against Ismaily, handing the title to Al Ahly for the fifth time in row and rewarding himself with the second personal title of the Egyptian Premier League Top Goalscorer, for the third time as a foreign player in the Egyptian Premier League history after John Utaka with Ismaily during the 2000–2001 season, then Flavio himself formerly during the 2006–2007 season.
At his time with Al Ahly he was very known in Egypt for his heading accuracy and it was known that Al Ahly played a tactic that Flávio Amado's fellow Angola national football team and Al Ahly teammate Gilberto would play a long ball to him from the sides, and Flávio Amado would score with his. He did this on multiple occasions, earning Al Ahly multiple titles domestically and continentally.
Qualified for the 2006 World Cup with Angola for the first time ever, and scored Angola's only World Cup goal in their history so far (despite playing for only thirty-nine minutes during the whole tournament).