The US businessman had claimed that the £230m European Offshore Wind Deployment Centre (EOWDC) would ruin the view from his golf course at Menie. As a result, he wanted the decision to approve the ambitious project overturned.
However, on Tuesday, Lord Doherty rejected the tycoon's legal bid.
The Trump Organisation has said it will review the decision.
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In 2011, the Aberdeen Offshore Wind Farm Limited (AOWFL) applied for consent to construct and operate a deployment centre for testing offshore wind turbines in Aberdeen Bay.
The project consists of 11 wind turbines, with a maximum power generation of up to 100MW.
Responding to the ruling, a Scottish Government spokesperson said: "Scottish Ministers are pleased that the court has found in their favour.
"The proposed European Offshore Wind Deployment Centre is an important project for Aberdeen and North East Scotland. It will give the industry the ability to test and demonstrate new technologies to accelerate its growth.
"Aberdeen is already of global importance for hydrocarbons and this wind deployment centre cements its role in renewable offshore development, further positioning Aberdeen as the energy capital of Europe and a world energy centre."
(JP/MH)
