HMV in Lincoln will not face closure, but the stores in Boston and Scunthorpe will close along with 64 others in the UK.
In a list announced on Thursday, Lincoln was not earmarked for closure.
The closures, which are a result of HMV calling in administrators last month, will affect around 930 jobs across the UK.
Deloitte administrator Nick Edwards said: “As part of our ongoing review of HMV’s financial position, we have now completed a review of the store portfolio and have identified 66 loss making stores for closure.
“This step has been taken in order to enhance the prospects of securing the business’ future as a going concern.
“We continue to receive strong support from staff and are extremely grateful to them for their commitment during an understandably difficult period.
“All other key stakeholders remain very supportive and I continue to be hopeful of securing a future for the restructured business.”
HMV UK went into administration early last week due to increased competition with the online market and supermarket deals.
However Hilco, which already manages HMV Canada, bought the entertainment retailer’s debt off its banks, Lloyds TSB and Royal Bank of Scotland.
Hilco helps restructure a variety of businesses, and is still working closely with HMV’s administrators, Deloitte, to secure the future of the store.
For a full list of the closures, visit Deloitte’s website.