The two Kosovo nationals, whose identity has not been made public, had planned "suicide attacks with cars packed with explosives" on troops with Kfor, the Nato force in Kosovo, as well as "attack places frequented by citizens", a Pristina court statement said.
One of the suspects had Belgian nationality.
The pair have been taken into custody for a month, in accordance with local law.
About 300 Kosovo nationals have gone to Syria to fight for IS, more than 50 have been killed there and 130 have returned home, according to official figures.
In May a Kosovo court sentenced eight Islamists, mostly Kosovo Albanians, to up to 10 years in prison for plotting to attack the Israeli football team in a World Cup qualifying match in Albania in 2016.
In France this week two Chechens were detained as part of a terror inquiry opened in Paris in February.
Investigators intend to establish if one of both of them spent time in Syria.
The last terror attack in France was perpetrated by 20-year-old Franco-Chechen Khamzat Azimov.
He killed one person and injured five in a knife attack in Paris.
One of his friends, Abdoul Hakim Anaiev, has been charged with taking part in a terror plot.
A large contingent of IS fighters has come from the autonomous Russian republic.