Police are holding 24 boda boda operators following the burning of a matatu on Lang'ata Road on Saturday.
One of the suspects was found with a speaker that he stole from the destroyed matatu. They were expected in court to face various charges.
Police say another matatu was burnt on Jogoo Road on Saturday night, terming the trend "unacceptable".
The matatu drivers were accused of having knocked and killed motorcycle riders at the sites where the vehicles were burnt by boda boda goons.
Inspector General of police Joseph Boinnet said they were concerned at the manner in which the operators behave in the city.
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"We wish to warn that this hooliganism, disregard of traffic laws as well as other penal code laws will not be tolerated," said Boinnet.
He said the police had been instructed to deal firmly with all law breakers including gangs pretending to be boda boda riders who wilfully destroy property whenever a road accident involving one of them occurs.
Boinnet asked for public support in taming the behaviour.
The drivers of the matatus were speeding to the city centre when they separately hit boda boda riders, killing them on the spot.
And when they stopped to attend to the riders, angry crowds attacked them before they set their vehicles ablaze.