Thomas and Sandra Gormley, of Cathkin, near Glasgow, have reached an out-of-court settlement with prosecutors to surrender the sum.
The pair are the latest to agree to pay out after negotiating a deal with the Crown Office's Civil Recovery Unit (CRU) – despite not being convicted of crime.
The unit – dubbed "secret squirrels" by their colleagues – alleged the Gormleys had profited from a mortgage fraud and that Mr Gormley alone had made money through his "involvement in drug dealing".
The out-of-court settlement was signed earlier this year, but like all such agreements was not published.
A Crown Office spokesman said: "In 2012 the Scottish ministers entered into an extra-judicial settlement with Thomas and Sandra Gormley, in terms of which the ministers have secured the recovery of certain property held by the Gormleys, namely an endowment policy, money in two bank accounts and a share of a house in Rutherglen.
"The extra-judicial settlement has not yet been fully implemented but the property to be recovered is worth approximately £90,000.
"The CRU, on behalf of the Scottish ministers, alleged that the property had been obtained through Thomas Gormley's involvement in drug dealing and both parties' involvement in fraud."
Solicitor Calum Ross, speaking for Mr and Mrs Gormley, said: "We do not accept that Mr Gormley profited through drug dealing."
The out-of-court settlement came six years after the Crown obtained a court order preventing the Gormleys from selling their detached twin-garage home in Rannoch Wynd in Cathkin, near Rutherglen, in 2006.
The CRU initially also targeted a series of other properties belonging to the Gormleys, including flats in Glasgow, Castlemilk and Rutherglen.
The Civil Recovery Unit has carried out several high-profile actions in recent months against people it believes have profited from crime.
The unit takes civil actions against alleged crime associates. So it only needs to makes its case on the "balance of probabilities" – not the tougher criminal proof of "beyond reasonable doubt".
In many cases, including that of the Gormleys, it settles out of court rather than get bogged down in lengthy judicial proceedings.
In June the Evening Times revealed the CRU was trying to seize the home occupied by Glasgow gangster Jamie Daniel.
The £350,000 property in Jordanhill was in the name of another man, Arthur Martin.
Strathclyde Police in recent months has also stepped up its efforts to pinpoint dirty money.
In the first quarter of the year the force – with the help of the Crown – seized a record sum of more than £9million in cash or assets.