Leyton Orient say they have paid all salaries and cleared their debts to Her Majesty’s Revenue and Customs.
However, BBC London understands some freelance contractors at the club are still yet to be paid.
Orient staff were not paid their wages for March on time, forcing some to relocate as they were unable to make rent or mortgage payments.
Owner Francesco Becchetti has been given until 12 June to sell the club or pay off all his debts to creditors.
In a statement on 24 April, the English Football League said it had asked the club for a “further commitment” that funds would be put into the club to pay staff and avoid the winding-up petition, but that they had not received a response.
Former owner Barry Hearn also resigned from his role as honorary president, saying he “could not be associated with any company that does not pay its staff their due wages on time”.
The O’s have already been relegated ahead of their final game of the season on Saturday, with a 3-0 defeat at Crewe on 22 April ending their 112-year stay in the football league.