But now Sheik Mohammed's racing empire faces a crisis, with news that a top Godolphin trainer was charged in connection with one of the biggest doping scandals to hit British horse racing.
On Thursday, the British Horseracing Authority banned Mahmood al-Zarooni for eight years after he admitted giving anabolic steroids to 15 of his horses at stables in Newmarket, England including 1000 Guineas favorite Certify.
The 15 horses also were banned from racing for six months dating back to the testing on April 9.
Al Zarooni, a former stable groom who was one of two British-based trainers for Godolphin, has been in trouble in the past. He was fined $3,000 in August after urine samples taken from two of his horses were found to contain a banned substance.
Sheik Mohammed has said he was "appalled and angered" to learn about the latest allegations.
"It is inevitable that Godolphin, as the trainer's employer, will have suffered damage to its reputation," Rupert Arnold, chief executive of the National Trainers Federation, said in an email to The Associated Press. "A more accurate picture will emerge from the evidence given at tomorrow's hearing.
Sheik Mohammed is the face of Godolphin and this scandal threatens to undo the work done in building one of the world's biggest stables and using it to showcase Dubai, a city of glistening skyscrapers that has emerged from the desert.
Godolphin has had enormous success, with its horses winning in 12 countries and earning more than $1 billion prize in money in the past five years. Al-Zarooni, who became a Godolphin trainer in 2010, trained the 2012 Dubai World Cup winner Monterosso.
"In terms of size it is a very important constituent, not only to the UK but in the rest of the world," said Alastair Donald, managing director of the UK-based International Racing Bureau. "It is massive in terms of its success. The number of graded stakes, which are important races, they have 200 Grade 1 winners which is more than anyone else."
Godolphin on its website describes Sheik Mohammad as its "driving force" and the stables allow him to showcase his love for horses, a theme that runs through the entire ruling family. He and several of his sons have been regulars on the endurance racing circuit races that can stretch more than 60 miles, often in desert conditions. One of his wives, Princess Haya of Jordan, is the president of the International Equestrian Federation and campaigned to clean up the sport.
But Princess Haya had a setback in 2009 when Sheik Mohammed was banned by the federation from riding in endurance races for six months after his horse twice failed doping tests.
Trainer Abdullah bin Huzaim acknowledged giving the horse drugs without the sheik's knowledge before the 75-mile desert races at Bahrain and Dubai. Bin Huzaim was banned for 12 months and fined $3,750 plus $1,585 in costs.
Sheik Mohammed is not alone among UAE riders accused by the equestrian federation for doping. According to its website, 31 riders in the UAE have been sanctioned since 2005 for either using banned substances or incorrectly using controlled medications during competitions. Some of those substances are permitted out of competition.
Among those punished was a son of Sheik Mohammed, who was disqualified from a 2006 race after his horse was found to have been given a banned substance.
Godolphin's case involves traces of two anabolic steroids drugs that can last several weeks in a horse's system. They are banned in Britain but other authorities allow them to be prescribed out of competition, including the UAE and Australia.
Donald said many people believe al-Zarooni acted alone and the reputation of Sheik Mohammed and the industry as a whole will emerge from this largely unscathed.
Sheik Mohammed, like his wife, has recently been an advocate of drug-free racing. He withdrew his representative last month from the Breeder's Cup committee after members backtracked on promises to ban the use of the diuretic Lasix, which prevents bleeding.
"It certainly is quite a sensation at the moment," Donald said. "But the racing industry as a sport is bigger than any individual party. Racing will move on and put this behind it, and I suspect Godolphin will as well."
Hours after al-Zarooni was charged, Sheik Mohammed said he was locking down the Moulton Paddocks in Newmarket and ordered blood tests for all the horses there.
"I can assure the racing public that no horse will run from that yard this season until I have been absolutely assured by my team that the entire yard is completely clean," he said. "I have worked hard to ensure that Godolphin deserves its reputation for integrity and sportsmanship, and I have reiterated to all Godolphin employees that I will not tolerate this type of behavior."