Belgian authorities say the plot required "immediate intervention".
The dozen suspects were arrested on Friday and Saturday as police raided 40 houses across Belgium.
Homes and garages were searched in 16 different municipalities, mostly in and around Brussels and including the area of Molenbeek.
A total of 40 people were questioned during the swoop, the federal prosecutor's office said in a statement.
There were no major incidents during the raids and no weapons or explosives are thought to have been found.
A statement from the prosecutors office said: "In connection with a criminal investigation concerning terrorism...40 persons were taken for questioning.
"Twelve among them were arrested. The investigating judge will decide on their possible detention later today.
“Evidence was gathered [and] as part of the instruction [we] needed to intervene immediately."
Prosecutors also say they have arrested a Belgian national in connection with the Brussels Terror attacks on March 22.