RSPB Scotland has been refused permission to appeal against a ruling which allows an offshore wind farm to go ahead.
The charity objected to developments in the firths of Forth and Tay which it said threatened thousands of sea birds.
An earlier successful challenge to the projects was overturned after the Scottish government lodged an appeal.
The RSPB wanted to take this decision to the Supreme Court, but judges rejected the bid.
The decision was made by a panel of three Supreme Court Justices following a review of the written submissions.
Permission was refused on the grounds that the application did "not raise an arguable point of law of general public importance".
The judges also noted that the case had already been the subject of a judicial decision and reviewed on appeal.
Scottish ministers approved the Inch Cape, Neart na Gaoithe and Seagreen Alpha and Bravo projects in 2014.
It has been estimated that they could generate up to £1.2bn for the Scottish economy and power 1.4 million homes.
But RSPB Scotland raised concerns that the wind farms risked birds like puffins, gannets and kittiwakes.
The conservation charity said it was "extremely disappointed" by the decision to refuse permission to appeal.
Anne McCall, director of RSPB Scotland, said: "We have worked on the Firth of Forth and Tay projects for nearly a decade to try and ensure that they progress without causing unacceptable harm to our internationally-important seabird colonies.
"If these consents and their predicted impacts are realised, there is little doubt these would be amongst the most damaging offshore wind farms for seabirds in the world.
"In addition to these enormous risks to wildlife, we had major concerns with the assessment methods and the approach taken by Scottish ministers. Due to these concerns, RSPB Scotland felt there was no other option but to judicially review the ministers' decisions."
Ms McCall said the RSPB would take some time to consider "all other options" that remained.
Work on the wind farms is expected to begin next year.
One of the developers, Mainstream Renewable Power, said the RSPB's legal action had delayed its project by two and a half years.
Chief executive Andy Kinsella added: "We are delighted with the decision and look forward to working constructively with RSPB Scotland to take the wind farm into construction next year.
"This project was consented by Scottish ministers in October 2014 on the advice of Scottish Natural Heritage and Marine Scotland.
"We have been rigorous in our approach throughout the project, working with partners and supply chain businesses to find the best possible way to deliver the project. We look forward to seeing Neart na Gaoithe up and running."
The Scottish government has also said it was keen to "work constructively" with stakeholders like the RSPB to protect wildlife while developing a "vital low-carbon resource".
A spokesman for the other developer, Red Rock Power, said the company welcomed the court ruling.
"Red Rock Power also acknowledges the important and continued role that RSPB has in protecting our internationally important seabird populations," he said.
"We will therefore continue to work collaboratively with the RSPB and all stakeholders to refine the project design to ensure that the project can be delivered whilst minimising environmental impacts."