The estate was founded in 1997 by one of the leading figures in the Greek wine industry, Yiannis Boutaris, after leaving his family's Boutari Wine Group. It is now led by Stellios Boutaris, the fifth generation of winemaking Boutaris.
The new estate consisted of various vineyards previously accumulated by Yiannis Boutaris. 40 hectares (100 acres) of Xinomavro were planted in 1970 and formed the main estate. The white wine vineyard in the Amyndaio (Amyndeo) region was planted in 1985. An old winery was bought in 1996.
Between 2004 and 2006, 28 hectares (70 acres) was replanted. Some new Greek and international varieties were introduced, as well as some different clones of Xinomavro best suited to the various vineyard sites. A further 10 hectares was purchased in 2009. This made Kir-Yianni one of Greece's largest vineyards.