Abubakar Saalim Kitonga did not however plead to any charge after investigators asked the court to detain him for a further 30 days.
Kitonga is linked to attacks on a bus and another at a quarry that left at least 60 people dead.
The investigators say Kitonga is believed to be an al-Shabaab agent based in Mandera responsible for recruiting and organising movement of the militia in and out of the country to execute attacks. READ: Suspect in Mandera killings arrested, flown to Nairobi.
The court also heard that the terror suspect is believed to be sneaking explosives into the county.
Senior Principal Magistrate Ellena Ndiritu was told that investigators will head back to Mandera with the suspect, Western and Eastern Kenya where he traces his roots.
The court allowed the investigators to detain Kitonga for a further 14 days but will grant them a chance to apply for more time if they are unable to conclude investigations within that period. READ: 36 people killed in another Mandera attack.
The terror suspect has also been implicated in the spate of other attacks in the Northeastern region.
Police said they have evidence linking Kitonga to the planning of the two attacks in Mandera and other terrorist activities.
The 30-year-old suspect is reported to have been living in a mosque within Mandera town, where he was arrested and taken to the regional police headquarters in a covert operation.