Met Police Assistant Commissioner Mark Rowley said the activity would be led by Portuguese police with the involvement of British officers.
Madeleine was three years old when she went missing from a holiday apartment in Praia da Luz, Portugal in May 2007.
Scotland Yard launched a fresh investigation last July.
Mr Rowley did not give details about what the next phase would involve, but said officers were working through every credible line of inquiry as part of the "slog of a major investigation".
He said: "It's something that you would expect in any major inquiry.
"A thorough serious crime investigation works systematically through all the credible possibilities, and often in an investigation you will have more than one credible possibility.
"Therefore just because we're doing a substantial phase of work in the forthcoming weeks doesn't mean that it's going to immediately lead to answers that will explain everything."
The Metropolitan Police's relationship with officers in Portugal was working well, he added.
Scotland Yard's investigation - codenamed Operation Grange - came two years into a review of the case.
In March, British police said they were seeking an intruder who sexually abused five girls in Portugal between 2004 and 2006.
Detectives say the attacks happened in holiday villas occupied by UK families in the Algarve.
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Police investigating Madeleine McCann's disappearance say "a substantial phase of operational activity" will begin within weeks.