There were fears that the club could have gone into administration if they had to pay Bloor Homes £580,000 as a contingency against a possible maximum Section 52 payment.
Nuneaton and Bedworth Council decided that on payment of a fee of £250,000 the covenant would be lifted.
Boro will open their new Liberty Way home on July 17th against the Sky Blues who will stage some reserve team matches there.
Their Chairman Roger Stanford told the BBC: "We're just pleased to be able to move on now. "It means that we can now progress to the next stage, which is to start turning the club into a community club."