In the wake of the 1999–2000 season he became a member of Agios Nikolaos, a second division club and won the respect of president Lampros Maris whom Kyrgiakos considers as his second father.

The centre-back injuries at his parent club, Panathinaikos, just before the Third Qualifying round matches with Slavia Prague for the 2000–01 Champions League meant that he had to return to Paiania and become a regular member of the starting line-up.

With his new club, he won a second consecutive championship and also the Scottish League Cup, scoring two goals in the 5–1 win against Motherwell in the final.

[9] In his first season, he proved to be a fan favourite with some great performances and crucial goals which helped the team avoid relegation.

On 1 July 2008, after his two-year deal expired, Kyrgiakos decided not to renew his contract with the German club, and so was released.

He stated, "The big pony-tailed Greek put in a sterling performance at The Britannia and may typify the less football, more grit of the new Reds... And it is no-nonsense men such as Kyrgiakos who like to roll up their sleeves which can keep Rafa in a job right now.

"[17] Kyrgiakos' fine form continued in the very next game as Liverpool kept a clean sheet in a 0–0 draw away at Wolverhampton Wanderers on 26 January 2010.

[19] Meanwhile, the legendary Liverpool striker Ian Rush also praised Kyrgiakos, stating that he is ready to fill the void left behind by Sami Hyypiä.

Saunders stated Kyrgiakos' "physical presence in the heart of the defence has been key to a spirited resolve in recent matches.

Teams are having to work hard to score against Liverpool, which hadn't always been the case before Kyrgiakos' sustained run in the side.

On 16 September, he partnered Daniel Agger at centre-back for the Reds' first Europa League group game against Steaua București at Anfield, Liverpool cruising to a 4–1 win.

As instructed by the manager, Kyrgiakos had recently been played up front as a target man at times when Liverpool had been down in the final minutes and needed a goal.

Kyrgiakos stated in the press conference, "It's a beautiful thing for me to come to Sydney and play football in Australia.

He made his debut for the club on 23 March 2014 in round two of their NSW State League match against Blacktown Spartans at Belmore Sports Ground, where they lost 3–1.