Appleby secured his first Group stakes success with Cap O'Rushes in the Gordon Stakes at Glorious Goodwood on Wednesday, having only received his licence from the British Horseracing Authority (BHA) last Thursday.
Previously, the influential Dubai-based organisation had employed only Emirati trainers at Newmarket, with Al Zarooni joining Saeed bin Suroor.
Hilal Ibrahim preceded them during the infancy of the global racing operation in the early 1990s.
Appleby, who was born on the south coast of England, has been with the international stable for 15 years working under Bin Suroor and, more recently, Al Zarooni, who was fired over his role in a doping scandal in the spring.
"It was important to have somebody in-house who understood Godolphin and understood what we were trying to do," Godolphin's Simon Crisford said. "Charlie has worked his way up to the top and has been a great asset to Godolphin since Day 1 and was the most suitable candidate available to us."
Crisford refuted the suggestion that the organisation he runs as racing manager would consider having more horses with other trainers from the end of the season, such as the agreement that resulted in Dawn Approach remaining with Jim Bolger in Ireland.
"Everything has happened so quickly this summer and everyone needs time to find their feet, including Charlie, and we will cross each bridge as we come to them," Crisford said.
Following the BHA investigation into the doping practices at Moulton Paddocks, which resulted in 22 horses receiving bans for six months, Godolphin initiated an internal investigation.
The report has been passed on to the regulatory body.
No details of that report will be made public.
The BHA report, however, made nine recommendations that centred on poor middle management at Godolphin, focusing mainly on Moulton Paddocks.
Those changes were initiated by Bin Suroor when he took charge of both stables at Newmarket after Al Zarooni was banned for eight years in April.
At the news conference that followed Al Zarooni's hearing, Crisford refused to offer his resignation, stating that as racing manager he was not answerable for practices at each and every stable in which Godolphin has horses.
Godolphin have around 400 horses at Newmarket, as well as horses in training with Andre Fabre in France, and Tom Albertrani, Eoin Harty and Kieran McLaughlin in America.
In Dubai, they have the Al Quoz and Marmoom stables, and in the wider context, the Darley operation in Australia and Sheikh Hamdan bin Mohammed's runners with Mark Johnston in England.
"All the issues that needed to be addressed have been addressed," Crisford said of the doping fallout. "When the incident occurred, Saeed took over and transformed it to the way that his stable is run.
"We all understood the importance of time taking its course. The BHA underwent their investigation in a very detailed and thorough manner.
"The criticisms they laid on at our door were fair and valid.
"We are moving forward."
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