The two flats were situated in Berlin's Neukölln and Friedrichshain neighbourhoods.
City prosecutors had given the green light for the operation after the residents of the apartments were suspected of planning a terrorist attack and possessing illegal weapons.
One of the suspects is a 28-year-old: investigators found photographic evidence of him posing with an AK-47 and who alleged proclaimed his desire to travel to Syria to take part in the civil war there.
Investigators seized mobile phones, a laptop, an air gun and several other objects which they claim contravene the country's weapons prohibition laws.
Meanwhile police in North Rhine-Westphalia arrested a 31-year-old man at a refugee home on Thursday on suspicion of belonging to the terrorist organization Isis.
According to Bild newspaper, Syrians who are opposed to Isis published pictures of the man and police then reacted. Bild did not, however, name a source for its information.