The general prosecutor's office said that it was designating Meduza an "undesirable" entity.
"It has been established that its activities pose a threat to the foundations of the constitutional order and the security of the Russian Federation," prosecutors said.
Meduza had already been branded a "foreign agent" in Russia in 2021.
It is the first time a major media outlet with millions of readers has been labelled "undesirable" and outlawed in the country.
Russian authorities have been presiding over an unprecedented media and opposition crackdown since President Vladimir Putin sent troops to Ukraine in February.
Established in 2014, Meduza is based in Latvia to circumvent Moscow's censorship.
Under the "undesirables" law, Russians who maintain ties with such organizations could face heavy fines or prison terms of up to six years.
The designation can have serious consequences not only for Meduza's reporters and editors but also interviewees and readers who share its stories on social media.
In a statement, Meduza urged Russians to keep reading their stories and pledged to resist the pressure.
"We would like to say now that we are not afraid, and we do not care about the new status -- but this is not true," it said.
"We are afraid for our readers. We are afraid for those who have worked with Meduza for many years. We are afraid for our loved ones and friends."
Independent Russian journalists expressed support, saying the prosecutors' label meant that state propaganda was not working.
"It is the first time that the state is directly seeking to exterminate an outlet with millions of followers, the main independent source of news and stories for Russian-speaking readers," Novaya Gazeta Europe said.
Several media outlets have been labelled "undesirable" in Russia in the past.
Since Putin sent troops to Ukraine, all independent media in Russia have been closed or have suspended activities.
Access to the websites of foreign-based media, such as Meduza, has been restricted.
The "foreign agent" label -- reminiscent of the "enemy of the people" of the Soviet era -- has in recent years been used extensively against opponents, journalists and rights activists in Russia.
On Wednesday, a Moscow court ordered the closure of Russia's oldest human rights organization, the Moscow Helsinki Group.