Barney Harford, the chief operating officer, and Rebecca Messina, the chief marketing officer, are both leaving the company, Uber said, and the position of COO is being eliminated.
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Harford came under fire previous year after the New York Times reported on racist remarks he allegedly made during a conference call with other Uber employees.
"This will allow me to be more hands on and help our leaders problem-solve in real time, while also ensuring that we make our platform vision a reality", Khosrowshahi said.
Mr Harford, the exiting COO, has been shielded from the public spotlight after he was the subject of an internal review over what some employees described as racially insensitive remarks by the operating chief previous year, Bloomberg reported.
We've made so much progress over the last two years, and Uber is in a far better spot both internally and externally.
As part of the leadership shakeup, two additional executives - one representing the Uber Eats team and the other representing Uber's global rides business - will report directly to Khosrowshahi.
Mr Macdonald, who will lead operations, started at Uber in 2012 as a general manager in Toronto.
Harford was hired by former CEO Travis Kalanick and has been with the company for around 18 months.
Uber has under-performed in its first month as a public company, as investors question its ability to someday turn a profit.
Messina had been a beverage industry executive before coming to Uber. In its first quarterly financial report last week, Uber posted a $1.01 billion loss.
Uber shares that ended the formal trading day down slipped 1.2 per cent to $43.63 in after-market trades.
"Our brand continues to be challenged", Khosrowshahi said in the email.
He cited a need for a clear and consistent "narrative" at Uber when it comes to how the company is seen by consumers, partners, policymakers, and the press as a factor in his decision to consolidate the marketing, communications, and policy teams.