Ruai Ward MCA John Kamangu, who is also the deputy speaker, takes over as Acting Speaker until a new substantive speaker is elected.
She cited power tussles, frustration and interference from Governor Mike Sonko as reasons for her resignation.
On his part, Deputy Speaker Kamangu expressed shock at the resignation saying he did not see it coming.
Nairobi County Assembly Speaker Beatrice Elachi has resigned.
The surprise move comes after months of wrangles at the Assembly that saw MCAs divided into factions, with some in her support and a majority opposed to her leadership.