Police and sniffer dogs descended on the house near Hanover, where suspect Christian Brueckner once lived, after receiving a tip-off from a member of the public.
Officers were on the scene from early on Wednesday morning, but the current residents of the house were found to be innocent citizens and the eight-hour search ended without any apparent breakthrough.
Authorities did not give any official explanation for the search, but local newspaper Neue Presse said it was linked to the Madeleine case.
Christian Brueckner (right) is prime suspect in the kidnap and murder of three-year-old Madeleine (left) in 2007 while she was on holiday in Praia da Luz
In July, German police searched a vegetable garden 12 miles away which was once occupied by Brueckner, digging up the allotment in a two-day operation.
The allotment was only a short drive away from an apartment block where Brueckner was registered while living in Hanover, and the ‘Havana Club’ bar which he is thought to have frequented is also nearby.
One gardener said in July that Brueckner had lived off-grid at the allotment in 2007 and talked about planning his return to southern Europe.
‘I remembered his face from the pictures in the news. And I remember his van and his dogs. I had completely forgotten about him up until then,’ said Wolfgang Kossack, 73.
German media says Brueckner received at least two criminal convictions from a Hanover court, one for forging documents in 2010 and another for theft in 2013.
He split his time between Germany and Portugal from 2013 to 2015, prosecutors in Hanover have said.
Brueckner lived in the Algarve for much of the period from 1995 to 2007, and German prosecutors say he received a phone call from a Portuguese number around the time of Madeleine’s disappearance in May 2007.
Police use rakes to search an allotment in Hanover this year where bags of evidence were taken away from a vegetable garden once occupied by Brueckner
Weeks after the allotment search, authorities indicated they had been looking for digital storage devices, but Brueckner’s lawyer accused them of ‘desperation’.
Since taking the lead in the case earlier this year, German police have struggled to explain what evidence they have about Madeleine’s disappearance.
Last week, a leaked memo revealed that Portuguese investigators were ‘shocked’ by the lack of concrete evidence after being briefed on the case against Brueckner.
Before that, there was confusion about whether German authorities had specific evidence that Madeleine was dead, as they initially implied they did.
Brueckner is currently in prison for an unrelated drugs conviction, and he is yet to begin a sentence for raping a 72-year-old American woman in Portugal in 2005.
In September, a European court rejected an appeal he had made on procedural grounds against his extradition from Italy to Germany in the drugs case.
This week it emerged that the 43-year-old was injured while being taken to a parole hearing in Braunschweig.
The Braunschweig court said he sustained injuries to his ribs when law enforcement officers were putting ankle cuffs on him before the hearing Monday.
The court said he was treated in hospital and the parole hearing took place, and he was later returned to prison.