Grubhub scrambled to fend off allegations that it’s been charging bogus fees to restaurants and setting up fake Web sites to take orders, even as it reported a 96-percent profit plunge.

On a Tuesday conference call with analysts, Chief Executive Matt Maloney pushed back on criticism of Grubhub’s treatment of restaurants and their customers, which has lately attracted the attention of New York regulators and Democratic Sen. Chuck Schumer.

“Any characterization that we are intentionally misleading or manipulating restaurants at their expense is patently false,” ­Maloney said.

The Chicago-based food-delivery giant — which also owns Seamless — said Tuesday its net income from March to June plummeted to $1.3 million from $30.1 million a year earlier, blaming surging operating expenses and marketing costs, which included perquisites like free meals.

Grubhub shares fell as much as 13.3 percent, to a low of $69.42, before ending the day down 12.3 percent, at $69.93.

In May, The Post exclusively reported that Grubhub was charging restaurants commissions as high as $11 for a phone call — even if a customer was merely calling to ask about store hours.

Restaurateurs have griped that the fees take advantage of small business owners, who work long days and don’t have time to vet whether a month’s worth of phone-related fees are legitimate.

Schumer told The Post in an exclusive interview this month that Grubhub’s practices were “unfair” and he wanted the company to give back the commissions.

But on Tuesday, Maloney stood by Grubhub’s requirement that restaurants dispute every sham commission one by one. Grubhub gives back commissions for any bogus charges made in the last 60 days — if a restaurant owner spots them.

“We still allow restaurants to review telephone orders via their manager portal, so we are completely transparent; we believe this is fair,” he said.

Last month, one restaurateur told The Post that after being told by Grubhub he was only entitled to 60 days’ worth of refunds, he persisted and got $10,000 for several years’ worth of bogus charges.

During the roughly hourlong analyst call Tuesday, Maloney lashed out at critics and accused competing delivery services, without naming them, of creating a “Wild West” of rampant “price gouging.”

Maloney’s combative tone didn’t sit well with some in the restaurant business.

“It’s as if they’re going out of their way to infuriate their restaurant clients, instead of acknowledging their company’s problems and fixing them, which is really all restaurateurs want,” Andrew Rigie, executive director of the NYC Hospitality Alliance, told The Post.

Grubhub’s profits were eaten up by a 60-percent increase in sales and marketing costs, to $74.1 million. Operations and support also rose 59 percent, to $106.4 million,as it beefed up its order-tracking technology in its app.