Binny Bansal, chief executive of India's biggest online retailer, Flipkart, has resigned following an investigation into his conduct.
Flipkart and its owner, Walmart, launched the investigation after a complaint of "serious personal misconduct" was made against Mr Bansal.
The inquiry did not find evidence to back up the allegation, but did "reveal other lapses in judgement".
Walmart paid $16bn (£12.3bn) earlier this year to take control of Flipkart.
The companies did not give any further details about the allegation against Mr Bansal.
However, in a combined statement, they said he had shown "a lack of transparency" in his response to the situation.
In an email to staff, seen by the BBC Mr Bansal said: "The allegations left me stunned and I strongly deny them.
"These have been challenging times for my family and me. I am concerned that this may become a distraction for the company and the team. In light of these circumstances, I feel it is best to step away as chairman and group CEO."
Mr Bansal co-founded Flipkart in 2007 with Sachin Bansal who, despite sharing the same surname, is not related.
The firm, which sells everything from books to clothing and food, is now one of the biggest online retail players in India.
This year, Walmart announced it would take a majority stake in the company, drawn by India's fast-growing e-commerce market, which is expected to grow from its current size of $35 billion to $100 billion by 2022.
Goodbye to a backroom master mind
Analysis by Sameer Hashmi
Sachin Bansal and Binny Bansal are the poster boys of India's start-up dream.
In a country dominated by traditional family businesses, they started Flipkart in a two-room apartment, building it into India's first billion-dollar online retail company.
This year, the firm also became the country's most valuable start-up after Walmart acquired a controlling stake in Flipkart for $16bn.
For years, Binny Bansal - who previously worked at Amazon - was always the backroom mastermind, running operations while Sachin served as its designated leader.
But after becoming the chief executive of the company, Binny transformed from a "quiet" co-founder to the company's main face.
His resignation will be a blow for Walmart, which is locked in an intense battle with rival Amazon to garner more market share in India's highly competitive consumer market.
Sachin Bansal left the company shortly after the deal with Walmart.
The companies said that Binny Bansal had been considering leaving as well: "Binny has been contemplating a transition for some time and we have been working together on a succession plan, which has now been accelerated."
Walmart has praised Flipkart's leadership, saying it believed local expertise would give it a competitive edge.
The firm's statement said it remained "committed to investing for the long term and are supportive of the leadership team's desire to evolve into a publicly traded company in the future."
Kalyan Krishnamurthy, who now leads the firm's central e-commerce unit, will take over as chief executive.