Since the first-round vote in January, the election campaign has been upended by two weeks of storms and fierce gales that have killed at least seven people and created an estimated four billion euros ($4.7 billion) in damage.
The storm disruption forced around 20 of the worst-hit constituencies to postpone the vote by a week, but the election went head for nearly all the 11 million eligible voters in Portugal and abroad, starting at 8:00 am (0800 GMT).
First exit polls were due at around 8:00 pm, after the last polling stations in the Azores archipelago close.
Voters were being asked to choose between veteran Socialist Antonio Jose Seguro, who won most votes in the first round of the election in January, and extreme-right candidate Andre Ventura, who came second.
Ventura -- who trailed Seguro in opinion polls -- alleged the government's response to the fierce gales and floods had been "useless" and called for the entire election to be postponed.
The authorities rejected that demand and Seguro, during his last campaign rally on Friday, accused Ventura of "doing everything to keep the Portuguese from turning out to vote".
Seguro, 63, is a veteran political operator and former Socialist party leader.
Despite being out of the public eye for the past decade, one opinion poll on Wednesday credited him with 67 percent of voting intentions in the run-off election.
This predicted victory and the recent foul weather has raised concerns in Seguro's camp that many voters will stay at home.
At midday, turnout stood at 22 percent, slightly higher than at the same time of day during the first-round vote.
- Turnout -
Seguro urged voters not to abstain.
Casting his vote in Caldas de Rainha, where he lives, he said: "Come and vote. Make the most of this window of good weather."
His rival retorted that it showed "lack of respect to send people out to vote after what has happened".
Casting her ballot in Lisbon, retired teacher Celeste Caldeira told AFP she thought the authorities had "made the right choice to go ahead with the election".
"We have two candidates. Either we vote for the one who has everyone's interests at heart or I don't know where we're going," the 87-year-old said.
While Ventura, 43, has campaigned on a promise to break with the parties that have governed Portugal for the past 50 years, Seguro has positioned himself as a unifying candidate and warned of the "nightmare" the country could face if his opponent wins.
Seguro won the first round of the election, in which 11 candidates were standing, with 31.1 percent of the vote, ahead of the 43-year-old Ventura on 23.5 percent.
He has since secured the support of many political figures from the far left, centre and the right.
But Prime Minister Luis Montenegro -- whose minority centre-right government has to rely on support from either the Socialists or the far right to get legislation through parliament -- has declined to endorse either Seguro or Ventura in the second round.
Voting in Lisbon on Sunday, 20-year-old medical student Julia Rodrigues said she did not know who to vote for.
"It's a really difficult choice because I don't like either candidate," she told AFP.
- Political ambitions -
Ventura is the first extreme-right candidate to make it through to a run-off vote in Portugal.
His Chega (Enough) party, created as recently as 2019, became the leading opposition force at the May 2025 general election.
Analysts said that, while Ventura was expected to lose Sunday's vote, he would turn the election to his political advantage.
He is seeking to "assert himself as the true leader of the Portuguese right", political science professor Jose Santana Pereira told AFP.
Ventura has made no secret of his ambition to one day attain the powerful position of prime minister
In Portugual, the head of state has the power to dissolve parliament and call early elections but otherwise has a largely symbolic role.
The new president will succeed outgoing conservative President Marcelo Rebelo de Sousa in early March.
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