Police have flushed out Pastor Paul MacKenzie's wife from her alleged hideout in Mtwapa and placed her in custody.
Rhoda Mumbua Maweu now joins her husband in custody where he has been held over misleading his followers to fast in order to "meet Jesus".
Police said she was arrested alongside her aunt on Monday night.
Police pursued Rhoda after reviewing the Phone records of Pastor Mackenzie.
Police have been reviewing Mackenzie's phone records and interviewing individuals connected to the church.
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"She is a crucial figure in the church operation. An equivalent of 'human resource manager' for Mackenzie's administration," police said of the wife.
Rhoda is billed as a person of interest in the case as police say she is being probed over possible links to the Shakahola cult.
So far, at least 110 bodies have been exhumed from Shakahola forest believed to be owned by Pastor Paul Mackenzie.
Some 36 people have been rescued from starvation.
Police suspect that other victims could have been strangled to death.
On Sunday, President William Ruto said he will appoint a Judicial Commission of inquiry to probe the Shakahola cult deaths.
The commission, Ruto stated, will be tasked with establishing what led to the killing of the now over 100 people in the church owned by pastor Paul Mackenzie.
He was speaking during a church service at Makutano in West Pokot.