Karnataka police backed by Kerala counterparts arrested Madani at Anwarssery after he announced his decision to surrender before the Karunagapally magistrate court earlier in a press conference.
The police will now take him to Bangalore, where he would be produced before the Metropolitan Magistrate on Tuesday, Aug 17 evening.
The Bangalore blast accused's arrest came days after high drama.
Earlier in the day, speaking to media personnel, Madani had said that the case was a conspiracy.
"When I read about warrant in papers, I spoke to my lawyers. This is a conspiracy against me. I approached the court for bail as it is the right of every citizen," he said.