The £4.4 million facility for University of Sheffield, which has just received planning consent from the city council, boasts a series of small openings allowing boffins to study the insects as they fly in and out.
As well as a green roof, the scheme will also feature an adjoining 650m2 greenhouse.
Project architect Matt Hutton said: 'A bee flight room is integrated within the building, with holes in the wall linked directly to the bee flight paths, so their behaviour can be observed as they come in and out of the building.
'It is the first time we have been asked to include such a feature in a building. Usually we are required to keep bees and ants out of our buildings, not in.'
He added: 'These rooms have been designed to stay at a constant temperature, as many of the ants and other insects will be imported from hot climates.'
Building work is expected to start in June this year and is due for completion in summer 2008.