Sixteen people alleged to be part of Sharia4Belgium, including its head Fouad Belkacem, face charges of leading a terrorist organisation, the federal justice office said.
The remaining 30 will be tried on charges of belonging to Sharia4Belgium, it said.
However, only eight of the 46 ordered to face trial are currently in Belgium, scene last month of an attack at a Jewish museum in Brussels that left four people dead and shocked the country.
The others are believed to be in Syria where some of them may have been killed, the federal justice office said.
"The trial is likely to take place in September, at the earliest," a judiciary spokesman was quoted as saying by the Belga news agency.
In 2012, it said it was disbanding but the authorities suspect that it has continued to recruit dozens of volunteers to fight in Syria.
The attack at the Jewish museum in the centre of Brussels has raised fears of a resurgence of anti-Semitic violence in Europe and of terror strikes from foreign fighters returning from Syria.
Belgium has been active in working with its EU partners to tackle the problem and leaders of the G7 industrialised nations recently also agreed to take up the issue.