It has been revealed some 35 bats of various species have taken up residency in the tunnel under the 19th century Whitworth Flour Mill, which stands by the River Nene.
There are also believed to be four species of bat active within the vicinity of the mill.
Details of the bat colony has emerged five weeks after the historic mill and a 1.41 acre site were put on the market.
It is hoped developers can be sought to transform the four-storey mill into residential use, or a mix of residential accommodation and commercial use, which ideally would be a venture to promote the arts or design and media.
The surrounding land could be used for flats and/or townhouses.
The site is expected to be sold by way of informal tender with the closing date for bids set at January 17 next year.
But, any developer or owner would have to comply with a raft of regulations designed to protect the bats.
A spokesperson for Peterborough City Council said: “The presence of bats in the tunnel underneath the building would not stop the building from being developed, however it does mean that the developer would have to adhere to certain conditions to limit the impact on bat populations.
“There would be the ongoing legal requirement to ensure bats remain unaffected by any development or use of the building.
“However this should all be covered by the planning permission and conditions - the main issues will be during any construction activities.
“Post development it will be about avoiding disturbance from things like external lighting.
“However ‘normal’ activities and use of the building are unlikely to be in any way restricted.”
There are believed to be around 30 Daubenton bats and a small number - about five -common pipistrelle bats roosting in one of the tunnels beneath the building.
In addition, there are around four species of bats that have been found to be active within the vicinity of Whitworth Mill.
The spokesperson said: “All bats are protected and this legislation has been incorporated into our planning policies.”
Under planning conditions set out for the mill site, developers would have to secure a European Protected Species licence from Natural England and limit the works to the underground tunnel where the bats are roosting.
They would also have to install bat roosting bricks in the building during its development and employ an ecological clerk, install low-level light at the tunnel opening and monitor the bat population after construction.
Julian Welch, director of Peterborough commercial agents Barker Storey Matthews, which is acting on behalf of the council, to sell the site, said: “We have strong levels of interest. Informal tender bids are to be submitted by noon on January 17.”