The transfer, which formally took place today is part of the changes contained in the 2016 Scotland Act.
It means ministers at Holyrood now have control over thousands of hectares of rural land, around half of Scotland’s foreshore and leasing the seabed for rights to renewable energy.
The assets were worth a total of £271.8 million in 2015/16 and generated a gross annual revenue of £14 million.
The Scottish Government said the transfer will give communities a stronger voice over how those assets are managed.
Land Reform Secretary Roseanna Cunningham said: “This is a historic day. The management and resources of the Crown Estate now rest with the people of Scotland and we have a genuine, once in a lifetime opportunity to use them to change the fabric of Scottish society, placing the needs of local and coastal communities at the centre of our long-term planning for these considerable assets.
“From today, decisions about both the day-to-day management and the future of the estate will be taken in Scotland.
“This will have positive implications, not only for the many people who live, work or have some other direct connection with the Crown Estate, but for many communities across Scotland.”
A new body, Crown Estate Scotland (Interim Management), is taking on the role of managing the asset.