Council pest controllers cordoned off a section of Briggate on Wednesday morning after hundreds of the insects were seen swarming outside Marks and Spencer.
It is thought the bees were in a docile state and posed little threat to the public.
But beekeepers were called to remove them – and further swarms on Boar Lane and Duncan Street.
A spokesman for Leeds City Council said: “We received reports earlier this morning regarding a swarm of bees which had settled on a hanging basket on Briggate.
“A cordon was put in place and we dispatched a qualified beekeeper who has now gathered and safely relocated the bees. The cordon has now been removed.”