Brian Roy today announced his departure from the role of as general secretary after five years in the post.
He says he wants to move on to "new challenges", but it comes after a furious row broke out in the Scottish party ranks over a second independence referendum.
The Scottish Parliamentary Labour party issued a stinging rebuke yesterday, which said Mr McDonnell had undermined Scottish leader Richard Leonard - but left-wing MSP Neil Findlay hit back accusing PLP chair Jackie Baillie of abusing her position.
Mr Roy has worked for the party for 12 years, under four UK Labour leaders and seven Scottish leaders.
"It is time for me to move on to new challenges," he said today.
“Having been at the very centre of Scottish Labour during the most turbulent political times, I have worked hard to unite the Party, drive our campaigns forward, develop and diversify our candidates, and modernise our campaign machine.
“It has been a privilege to work with Labour Prime Ministers and a Labour First Minister, with many leaders in between, and I sincerely wish Richard Leonard and Jeremy Corbyn the very best as they prepare to win again as a Party of government.”
Mr Leonard thanked Mr Roy for his "dedication and hard work" for the party over the past 12 years.
“His extensive knowledge of, and loyalty to, the Labour Party, and his passion for our values, remains undiminished," he said.
"He has led the party organisation and the party’s staff as our general secretary through a very turbulent time."
UK leader Jeremy Corbyn, Leader of the UK Labour Party, said Mr Roy's "experience and knowledge has been invaluable" to Scottish Labour.
“Brian is Labour through and through," he added.
“The last thing they need is more interference from their madcap extremists in London.
“Barely a week goes by when a good person doesn’t jump from the Labour ship, and it just inflicts deeper wounds from which they won’t recover.
“If Scottish Labour can’t even stand up against their own party, how can anyone expect them to stand up to the SNP?”