Officers raided the idooPC computer shop and the Plum Tree hat shop, and a nearby flat. There were no arrests.
A West Yorkshire Police spokeswoman said: "The searches are part of an ongoing inquiry by officers from West Yorkshire Police and the Metropolitan Police as a result of inquiries into the bombings in London on July 7."
Neighbours said the two shops are owned and run by a Pakistani man and his white wife who live together in a flat above and have not been seen since Tuesday. Both shops, which are next to a BP filling station on the busy Dewsbury Road, were closed yesterday.
Police tape sealed off the alley behind them. The scene is a street away from the large Holbeck Police Station complex.
One nearby shop owner said: "The police arrived on Tuesday at about 5pm and there were quite a few of them. They were all wearing the usual white suits. They were here until earlier today."
The three premises are a few hundred yards from the home of Shahzad Tanweer, 22, one of the four bombers whose attacks killed 52 people. Two other attackers, Hasib Hussain, 18, and Mohammad Sidique Khan, 30, were also from the Leeds area.