In both city centres many businesses have remained closed. Demonstrators have also taken to the streets of other cities including Kisumu.
Human rights groups say since the protests against a controversial finance bill began two weeks ago 39 people have been killed by security forces.
President William Ruto has since dropped the proposed tax increases – but the demonstrations have morphed into calls for him to resign and anger over police brutality in the most serious crisis of his presidency.
The scale of demonstrations are smaller than last week’s, but chaotic scenes have been witnessed in Mombasa, where cars were seen burning as protesters clashed with police.
In Nairobi there is a huge security presence with running battles along some of the main roads leading to the centre. Groups of protesters lit fires and threw stones at police.
In the central business areas of Nairobi and Mombasa some shop-owners have hired vigilantes to patrol with clubs to guard against looting.
Astin Kibowen, 21, who is guarding the music shop where he works in Nairobi, told the BBC he wanted the president “to listen to our cries, to our voices”.
Since President Ruto came to power two years ago promising to revitalise the economy, Kenyans have been hit by a cost-of-living crisis with more taxes on salaries, fuel and on gross sales.
Linda Indakwa is using her art to show the impact of the protests in the capital
