I came across a brief but interesting article, Islam: A New Religion in a Traditionally Catholic Slovenia (1). My mom's family are originally from Slovenia (2); her grandparents came to America around 1900.

As the article on Islam mentions, Slovenia was kind of an odd country out in the old Yugoslavia: Catholic instead of Eastern Orthodox and speaking Slovenian rather than Serbo-Croatian. Slovenia broke away pretty quickly when Yugoslavia started breaking apart and seems to have done a good job of keeping itself largely out of the troubles that the rest of Yugoslavia descended into.

The Muslims in Slovenia are almost all Bosnian or Kosovar immigrants and refugees; that is, they've come from outside Slovenia.

Here's also a website (3) in Slovenian, which I can't read.