Just hours before the hand over ceremony in Pristina unknown attackers in northern Kosovo opened fire at vehicles of the EU-mission EULEX and Kosovo police, wounding a police officer.
This was the latest in a series of attacks on Kosovo police and international troops since Serb protesters violently clashed with KFOR troops in a border dispute last year.
Germany is a major contributor to KFOR and Halbauer is the fourth German general in row to lead the NATO-led troops in Kosovo.
Top NATO official US Admiral Bruce Clingan, a commander of the alliance's joint command in Naples, praised the KFOR troops as "enablers of progress here in Kosovo" adding that they reacted with "proportionality and restraint" to the risks and sometimes lethal threats in the tense north.
Also saluting the contribution of international peacekeepers to Kosovo, president Atifete Jahjaga said they gave to the citizens "the opportunity to shape our future in safe and secure environment".
Thanks to KFOR's presence in Kosovo "our country was able to overcome most of the consequences of war within a short period of time," Jahjaga said.
NATO launched its mission in Kosovo after the 1998-1999 war between the forces of then Serbian strongman Slobodan Milosevic and ethnic Albanian guerrillas. The conflict ended NATO planes ousted the Belgrade forces out of the territory.
Kosovo declared independence in 2008. It has been recognised by around 90 countries, including the US and all but five members of the EU. However, Serbia opposes the move, considering the territory as its southern province.
Kosovo Serbs, who make up the majority of the population in the north also refuse to recognise the ethnic Albanian authorities in Pristina.