The wildcat strike may be over, but the backlog of passengers will take time to clear.
Spanish airspace is open again after the government called a rare state of emergency and ordered the military to take over control towers.
Traffic controllers called in sick en masse on Friday in a dispute over pay and conditions.
They have now been forced back to work, but thousands are still desperately trying to catch flights.
One woman at Madrid’s Barajas airport, hoping to get a flight to Luxemburg, said: “I’m still here, and no one’s taking care of me. Even worse, they say to me go over there, and when I’m there they say go back over there.”
“I’m going to Greece for my brother’s wedding on Monday,” said another traveller. “At the moment I know nothing; nothing is clear, I’m waiting to know if it’s cancelled or not.”
The government is promising a strike like this will never be allowed to happen again and the controllers are being threatened with legal action.
Deputy Prime Minister Alfredo Perez Rubalcaba said:
“There will be consequences, no doubt about it, for all those who walked off the job in the control towers, in an inexplicable, irresponsible and damaging way.”
The action came after ministers approved changes to controllers’ working hours and a law that lets the military control air space in emergencies.
The selling off of part of the state airport authority has also been the focus of dispute.