The men were among about 20 detained in a series of arrests in Kosovo and neighbouring Albania and Macedonia ahead of the game in November, which was originally due to take place in the northern town of Shkodra.
The four are accused of planning to "carry out a terrorist attack against footballers and fans from Israel who were coming to Albania for the match in November," Kosovo's prosecution office said in a press release.
The match eventually took place in Elbasan, about 45 kilometres from the Albanian capital Tirana, under a massive security presence.
The prosecutors said two other suspects were charged with plotting terrorist attacks against local and international officials in Kosovo, while another was charged over fighting with jihadists in the Middle East.
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Another pair were charged with collecting weapons and illegally producing an explosive.
Kosovo, a predominantly ethnic Albanian and Muslim country, has been confronted with more than 300 of its citizens waging jihad in Syria and Iraq.