After Stewart left the club to join Gençlerbirliği, Žaliūkas was appointed club captain by new manager Jim Jefferies. Soon afterwards, however, Žaliūkas' future at Hearts was put in doubt due to failed contract negotiations, which resulted in him being left out of the team. However, in November 2010 signed a permanent contract, ending his previous loan agreement from Kaunas, which committed him to the club until the end of the 2013 season. Towards the end of the 2010–11 season he was once again left out of the team on the orders of club owner Vladimir Romanov. On 19 May 2012, Zaliukas lifted the Scottish Cup with Hearts after a historic 5–1 win over Edinburgh rivals Hibernian.