The stores, on Croydon High Street, Beulah Hill and Thornton Heath High Street, are labelled as legal suppliers of CBD cannabis supplements.
But MET Police raided them on Wednesday after suspecting the owners of selling cannabis containing psychoactive THC, which only licenced pharmacies can do.
Also removed from one of the shops were 63-thousand nitrous oxide canisters, some suspected magic mushrooms, 20-thousand pounds in cash and a Bitcoin ATM.