Bury will start the League One season with a 12-point deduction after entering a Company Voluntary Agreement, the EFL has announced.
The Shakers, promoted last season, saw a winding-up petition over unpaid debts adjourned at the High Court last month and have now secured their future with the CVA.
The club, however, will kick-off the forthcoming campaign with the points penalty.
"Following receipt of notice that the Company Voluntary Arrangement (CVA) has been passed in respect of Bury Football Club, the EFL can confirm that the club has now suffered an insolvency event and will be subject to a 12-point deduction," said an EFL statement.
"In accordance with EFL regulations, the sporting sanction will take effect immediately and the club will start the League One season on minus 12 points. The club has seven days to appeal.
"The EFL will now continue its discussions with the club's ownership with the aim of achieving a long-term future for the club."
Earlier on Thursday, Bury chairman Steve Dale revealed the cash-strapped club would be safe after agreeing the CVA.
Dale, who was involved in an angry confrontation with a group of supporters during Saturday's friendly at Nantwich Town, confirmed the news in a statement on the club's official website.
He said: "Today was a major day for our beloved club, the old girl is safe. The CVA was passed, so our future is secured, as I said I would.
"We have worked tirelessly to achieve the result today whilst taking a lot of flak. Some might say our methods were questionable but we can all pass comment with hindsight. My job was to save Bury FC and that's done. We have other hurdles but the main one is complete.
"Over the coming weeks, our fans will see the truth appearing once the police have completed their enquiries and arrests, and they will realise who had the club's best interest at heart. The facts as always will outweigh the social media spin and lies."
Dale, who revealed the club is working with the EFL to deal with outstanding issues, hit out at his critics and those who had brought his family into an acrimonious situation.
He said: "The social media garbage pedalled by the same few is not needed and bears no relation to the truth.
"I can't see how attacking my family has anything to do with Bury FC issues, but again it's the same mindless few.
"I accept emotions can run high – it's a passionate sport – but if we can put these things behind us and all get together, we will ensure our club has a great season in unity."
Bury begin their League One campaign at home against MK Dons on August 3. League One rivals Bolton will also start with a 12-point deficit due to their own financial problems.
