Adnan Hussain, who hails from Karnataka, Mohammad Farhan, from Maharashtra, and Sheikh Azhar Al Islam, from Jammu and Kashmir, were arrested by NIA after registering a case in New Delhi, official sources said.
The trio were deported from UAE and they were detained by the NIA upon their arrival in the IGI airport on Thursday night.
They will be produced in a court on Saturday. The three suspects along with other unknown associates were allegedly involved in a conspiracy to identify, motivate, radicalise, recruit and train Indian citizens located both in India and other countries for planning and executing terrorist attacks in India and in other friendly countries, sources said.
The youths believed to be members of the Abu Dhabi module of the ISIS.
On September 15, 2015, the UAE had deported four Indians suspected to have links with ISIS.
The UAE had also sent back last year a 37-year-old woman Afsha Jabeen alias Nicky Joseph who was allegedly involving in recruiting youths for ISIS.
In January 2015, Salman Mohiuddin of Hyderabad was arrested when he was preparing to board a flight to Dubai on way to Syria via Turkey.
According to Indian intelligence agencies, a total of 23 Indians have so far joined the ISIS of whom six were reportedly killed in different incidents in Iraq-Syria.
Among the 23 are two absconding members of the banned Indian Mujahideen who had gone from their hideouts in Pakistan.
The dead were identified as Athif Vaseem Mohammad (Adilabad, Telangana), Mohammad Umar Subhan (Bengaluru), Maulana Abdul Kadir Sultan Armar (Bhatkal, Karnataka), Saheem Farooque Tanki (Thane), Faiz Masood (Bengaluru) and Mohammad Sajid alias Bada Sajid (Azamgarh, Uttar Pradesh).
Around 150 Indians are under surveillance for their alleged online links with ISIS.
As many as 30 other Indians, who were radicalised by ISIS elements, were prevented from travelling to the conflict zone in the Middle-East.
Among those who are currently fighting for ISIS include two youths from Kalyan in the outskirts of Mumbai, an Australia-based Kashmiri, one youth from Telangana, one from Karnataka, one Oman-based Indian and another Singapore-based Indian.