In recent months Mr Donaghey had moved from being Europe supply director to supply strategy director for Diageo, which produces the likes of Johnnie Walker whisky and Smirnoff vodka in Scotland.
This followed an overhaul of its supply business announced in March which led to the axing of 80 roles across 50 of its sites in Scotland.
Under the scheme, Diageo's operations in Scotland became part of an Edinburgh-based international supply centre.
David Cutter, who previously headed up Diageo's supply operations in the Americas, was brought in to the run the centre, taking up the role on July 1.
Mr Donaghey was one of the principal public faces of Diageo when the company announced the closure of its Kilmarnock bottling plant with the loss of 700 jobs in 2009. He was also involved in expansion projects such as the building of the Roseisle distillery in Speyside.
He came to head up Diageo's supply business in Scotland in 2006 after a previous reorganisation when Diageo merged its spirit production business with that overseeing bottling and distribution.
Diageo said: "Bryan Donaghey served Diageo with great distinction throughout his time with the business.
"Bryan has severed his employment with Diageo and it is not appropriate to comment any further, but we wish him the very best for the future."