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Since the early 2000s, the European Academy of Sciences and Arts has been planning the establishment of the university, occasionally with the subtitle of European University for Leadership.
In 2010, Alma Mater Europaea was officially established, with Prof. dr. Felix Unger being appointed as its first president, while the German political scientist prof. dr. Werner Weidenfeld became the first rector, and the Slovenian lawyer and diplomat prof. dr. Ludvik Toplak the first prorector.
At a meeting in Munich in February 2011, under the patronage of the presidents of 12 member states of the European Union, the board determined which courses the university would provide. These were to be taught in various cities across the union, in several languages, including English, German, and Spanish. In line with the international nature of the university, students, teachers, and prominent European thinkers would meet at an international symposium at the graduation. It was also decided that Alma Mater Europaea would be incorporated in European and international networks of universities through cooperation agreements.
The university board stated that Alma Mater Europaea would be based on three so-called "W principles": Wissenschaft, Wirtschaft, Wirken. In German, this means: Science, Economy, Effect.
In 2011, the university opened in Slovenia its first campus, located in the Slovenian city of Maribor.