The ship featured in the Battle of Trafalgar in 1805, which is hailed as one of the most decisive naval battles of the Napoleonic wars.
It lies at the heart of Portsmouth's Historic Dockyard.
The estates of Dunecht, Haddo and MacRobert Trust have donated 10 oak trees and 11 elm trees.
The work is part of a 15-year conservation project.
HMS Victory - launched in 1767 - was built from more than 5,500 oak trees.
Andrew Baines, head of historic ships at the National Museum of the Royal Navy (NMRN), said: "Currently the ship comprises a variety of hardwoods from years of maintenance.
"The return to oak is much welcomed.
"It demonstrates the serious archaeological research we are undertaking about the ship's composition, from timber to paint analysis, and our commitment to ensure she remains sustainable for centuries to come.
"Interestingly, we understand that some 30% of the fleet at the Battle of Trafalgar hailed from Scotland, so it feels entirely appropriate that timber from these estates should be playing such a big part in her future security."
In 2013, a 3D map was created of HMS Victory, to better understand how to conserve it in the future.
Lord Nelson's flagship HMS Victory is to undergo renovations using timber donated by three estates in Aberdeenshire.