In a statement to AFP, senior political adviser Aquilino Morelle said he was stepping down but denied any wrongdoing.
"In the last 48 hours I have had to deal with insinuations and allegations calling my honour into question," he said.
"I want to reiterate that I committed no fault. I was never in a situation of conflict of interest," Morelle said.
"Nonetheless, I have decided to put an end to my duties as an adviser to the presidency of the republic... To be entirely free to respond to these attacks."
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Concerns had also been raised about Morelle's alleged extravagance at the presidential Elysee Palace, at a time when Hollande's government is asking French voters to accept spending cuts to rein in the country's deficit.
Mediapart reported that Morelle, the head of Hollande's communications operation, maintains a collection of 30 pairs of hand-made shoes at the Elysee that are professionally polished every two months.
Morelle has not contested the accuracy of the shoes revelation and has also confirmed Mediapart's claim that the two chauffeurs at his disposal were sometimes tasked with picking up his son from school, citing his "extremely busy schedule".
He had, however, denied the conflict of interest charges.
"At no point was I in a situation of a conflict of interest," Morelle wrote on his Facebook page in response to Mediapart's report. "As a civil servant, there are a certain number of outside activities which are permitted by the law, including education and advice."
Regardless of whether Morelle acted inappropriately, the revelations are deeply embarrassing for Hollande, who is struggling with the worst approval ratings of any French leader in modern times.