The men, all in the mid-twenties, had been on the radar of the police ever since they were turned back from Turkey four months ago. Kannur police said they were headed to Syria to join the terror organization when they were deported.
Over the next few months, the police closely tracked their online activities.
The three have been identified by the police as Mithilaj KC, 26, Abdul Razak KV, 24, and Rasheed MV, 27.
"We have been watching these youngsters for some time," said Kannur district's senior police officer PP Sadanandan.
"They were seen active on websites with links to ISIS and being were trained. We are probing for more details," Mr Sadanandan told media persons.
He said they were yet to figure how the men were recruited, the indoctrination methods and their funding.
Police said some more men, part of the same group, were also being probed.
They have been charged under the anti-terror law, Unlawful Activities (Prevention) Act, which outlaws people from associating and supporting a terrorist organization. If convicted, they could be jailed for a maximum of 10 years.
An estimated 100 Indians have left to fight for the Islamic State in Syria, Iraq and elsewhere, many of them from Kerala amid concerns that an extreme form of Islam was taking root in the state. In many cases, it was the families that reached out to the police for help.
The National Investigation Agency has been probing cases of disappearance of at least 21 people are suspected to have joined the ISIS. Among them, 17 were from Kasaragod and four from Palakkad. They include four women and three children.