Hospital officials said that numerous co-morbid conditions including heart diseases and kidney dysfunction resulted in her death.
Eman was under the care of 20 different doctors at Burjeel Hospital.
Ms Ahmed was later transferred to Burjeel Hospital in Abu Dhabi after disagreements between the family and staff at Saifee hospital in Mumbai over the cost of treatment and the amount of weight she had actually lost while she was an inpatient.
The 37-year old Egyptian woman weighed 1,102 pounds (500 kg), her family reported, prior to undergoing weight reduction surgery at Saifee Hospital in Mumbai in March.
Eman during her 37th birthday celebration earlier in September. She remained in Mumbai after the operation for several months. According to her family, Abdel Aaty had completed 25 years without leaving her home prior to traveling to India as she weighed 500kg.
Ms Ahmed had not stepped out of her house for more than two decades due to her weight and a stroke that left her paralysed a year ago.
She was brought to Mumbai from Alexandria, Egypt, on February 11 on board an Egypt Air fully-equipped cargo flight.
She was treated at the city's famed Saifee hospital by a team of around 15 doctors led by renowned specialist, Muffazal Lakdawala. On May 4, she was taken back to Abu Dhabi.
It is unclear whether Abd El Aty was undergoing a surgical procedure at the time of her death. "Her condition worsened in 24 hours and she suffered a multi organ failure", Dr Nahed Halawa, deputy medical director at Burjeel hospital, told the Indian Express.
Eman Ahmed Abd El Aty during a July 2017 news conference at Burjeel Hospital in Abu Dhabi. Her sister, Shaimaa Selim was involved in a dispute with the doctors who had even filed a police complaint against her for obstructing normal treatment of Eman. "We offer our prayers and honest condolences to the family of the deceas", the hospital said in a statement.