Inner Circle Investments, owned by Bolton Wanderers chairman Ken Anderson, has acquired Sports Shield's former 37.5% shareholding in the club.
Sports Shield BWFC Ltd was liquidated on 21 August after BluMarble Ltd lodged a winding-up petition in relation to non-repayment of a £5m loan.
Inner Circle holds 95% of shares after agreeing a deal with the liquidators.
In a statement, Anderson said a new arrangement had been reached with finance company BluMarble.
The loan to Sports Shield was secured against club assets and, because of accumulated interest, was thought to be closer to £7m.
"I am extremely pleased that this matter has been brought to a satisfactory conclusion and we can now all concentrate on taking the business forward without any further off-field distractions, which have been so publicly aired in the past," said Anderson.
"I would very much like to thank BluMarble for all of their co-operation in swiftly concluding the situation in respect of the outstanding loan.
"Throughout these negotiations their desire was to minimise any damage to the business and have remained very supportive of the football club.
"I'd like to thank all our loyal fans for their continued patience and support throughout this period."
Inner Circle and Sports Shield completed a joint-takeover of Bolton Wanderers in March 2016.
In May, Anderson said Inner Circle had acquired approximately 30% of Sports Shield to assist with resolving the matter with BluMarble, leaving Sports Shield with a 37.5% share in the Championship club and Inner Circle with 57.5%.
Former Bolton striker Dean Holdsworth, who owned Sports Shield, has resigned as a director of all group companies of the Championship club.