Early on Saturday morning, the airport said its scheduled 5am opening had been delayed due to drone sightings, advising passengers to contact their airlines.
"German air traffic control restricted flight operations at Munich Airport as a precautionary measure due to unconfirmed drone sightings and suspended them until further notice," a statement on the airport website read.
In a later update, the airport said 23 flights were diverted, 12 flights to Munich and 48 departures cancelled or postponed.
"As on the previous night, the airport and airlines took care of the passengers," it said.
"Camp beds, blankets, drinks and snacks were handed out."
The previous evening, the captain on a London-bound aircraft whose departure was cancelled told passengers that runways had been closed "because of drone sightings near the take-off and landing runways" and that police helicopters were aloft.
The airport website showed due arrivals had been diverted starting at 8.35pm.
Munich airport was closed for several hours late on Thursday and in the small hours after unconfirmed drone sightings that disrupted dozens of flights.
European aviation has repeatedly been thrown into chaos in recent weeks by drone sightings that some authorities have blamed on Russia.
The Kremlin has denied any involvement.
German Interior Minister Alexander Dobrindt promised earlier on Friday to bring forward legislation making it easier for the police to ask the military to shoot drones down.
