On Tuesday (3 November), HMRC officers arrested the men - aged 43, 48 and 37 - at their London addresses on suspicion of cheating the public revenue and fraud by false representation.
They mark the first arrests for alleged fraud relating to Chancellor Rishi Sunak's scheme to boost hospitality spending, which took place across August.
Kath Doyle, deputy director of HMRC's fraud investigation service, said: "The vast majority of businesses will have used Eat Out to Help Out responsibly, but we will not hesitate to act where we suspect abuse of the scheme.
"This is taxpayers' money and any claim that proves to be fraudulent limits our ability to support people and deprives public services of essential funding."
The EOHO scheme, which offered eat-in customers at participating hospitality venues a 50% discount up to £10 per person on all food and non-alcoholic drinks between Mondays and Wednesdays throughout August, was used to claim on more than 100 million meals, with some 84,000 individual restaurants registered to take part.