Now some closure might finally be near, not only for her family but also for the town itself.
Madeleine, then aged 3, disappeared from her hotel room during a family holiday in Praia da Luz in 2007.
On Thursday, German authorities said she was assumed to be dead and that an imprisoned German child abuser was the murder suspect.
It was the most significant development towards resolving the mystery of what happened to her after years of twists and turns. A long international investigation has grabbed attention worldwide but left many in Praia da Luz feeling like they had become pariahs.
"It was very complicated back then for everyone involved. Everyone spoke badly about Praia da Luz, especially among parents with children," said 40-year old Irina Itrabar, who owns a tiny beach store in the town of 3500 inhabitants.
"It was a tragedy for all of us. But some people have already forgotten what happened."
In the days and weeks after Madeleine's disappearance, members of the community rallied around.
Many helped the police in searches for clues in the surrounding area. Hundreds of people prayed in churches or gathered outside, flying balloons in a show of support for Madeleine and her family.
But the town also suffered a stigma. Business owners said some foreign tourists had been too scared to spend their holidays at Praia da Luz after she disappeared.
Looking at the ocean near a spot where he said friends of the McCanns had looked for Madeleine on the night she disappeared, 68-year old Luis Marques said he hoped the case was finally solved.
"I was here when the girl disappeared. It was very weird at the time. This changed everything. All the televisions were here. A very complicated environment was created," Marques said.
Some feared that, 13 years later, the new development could cast the town in a bad light again.
"Back then it killed all the business, just like the coronavirus," said 62-year-old German tourist Petra Michel.
"And people are trying to get back on their feet again and this whole thing is starting again."
