The Bombers announced on Tuesday they had been required to borrow $5 million to complete building of the High Performance Centre at Tullamarine.
The club said it had planned for the level of debt for the project, which had a total cost of about $25 million.
The AFL has helped fund the new base, as has the federal government, but the state government rejected the Bombers' bid for almost $5 million of funding last year.
The club's supporters and members have also been asked to help fund the new home, which boasts two ovals – identical in size to the MCG and Etihad Stadium – and an impressive indoor training facility.
The Bombers have been training there for more than a year. The club's administration staff is expected to move into the centre in October.
Essendon chairman Paul Little said the long-term debt plan was necessary.
"We have achieved over 70 per cent of our total fundraising target for the new facility thanks in part to many generous contributions to the Flight Plan campaign.
"However, the reality is we now need more help from our members and supporters to reduce this debt as quickly as possible."
Essendon will share the facility with the Australian Paralympic Committee.
The club suffered heavy legal fees during this season as it battled through the AFL-ASADA investigation.
In August, after the AFL Commission handed down its penalties to the Bombers, fining the club $2 million, Little said of his greatest concerns throughout the saga was the club's balance sheet as it funded its Melbourne airport facility.
Twitter: @AFL_CalTwomey
