Police have been scouring scrubland and abandoned structures near the town of Praia da Luz, where the three-year-old British girl went missing 18 years ago.
Officers could be seen holding pitchforks as they combed land in an area on the outskirts of Lagos in the Algarve on Thursday.
Search teams involving German and Portuguese officers, as well as firefighters, used pickaxes and shovels to dig undergrowth, and a digger was again used to remove rubble from an abandoned structure at the site.
They spent two days focusing on one particular derelict building, using a ground-penetrating radar on the cobbled ground after clearing the area of debris and vegetation.
British officers have not been present for the latest searches, the Metropolitan Police said.
German and Portuguese investigators could be seen shaking hands and embracing as the search drew to a close.
The officers stood in a circle for a debrief before taking part in a round of applause.
Authorities have not yet commented on the ending of the latest searches.
So far, officers have not announced they have found anything of significance.
Read more: What we know about new searches
German authorities had requested the search as part of their continued attempts to find evidence to implicate suspect Christian B.
The suspect, who cannot be fully identified under German law, is coming to the end of a prison sentence for the rape of an elderly American woman in Praia da Luz in 2005.
He has not been charged or indicted over Madeleine’s disappearance and denies any involvement.
It comes 18 years after three-year-old Madeleine disappeared from Praia da Luz while on holiday with her family in 2007.
She vanished after she was left sleeping while her parents, Kate and Gerry McCann, went for dinner in a nearby restaurant.
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