Rhoda Mumbua Maweu was arrested alongside her aunt from a hideout in Mtwapa on Monday night, according to police sources.
Investigations have revealed that Mumbua was a key figure in the church's operations, working as a "human resource manager" for Mackenzie's administration, and playing a significant role in recruiting new members into the cult.
Mackenzie has been accused of preaching a dangerous doctrine that encourages his followers to starve themselves to death in order to reach heaven faster.
The ongoing investigation has also linked Mackenzie to several incriminating messages found on his phone, exchanged with his wife.
Police have been reviewing Mackenzie's phone records and interviewing individuals connected to the church.
It was during this process that Mumbua's name came up as a person of interest.
Investigators believe that she played a vital role in recruiting new members into the cult and was involved in making financial decisions on behalf of the church.
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Mackenzie's church, based in the coastal town of Kilifi, has been under police scrutiny for several months, after members were found dead from starvation.
The cult's teachings included skewed and extreme religious practices, coupled with fear of the unknown.
The self-styled spiritual leader has been accused of manipulating his followers, leading them to their deaths in pursuit of salvation.
The arrest of Mumbua is a significant development in the ongoing investigation into the Kilifi cult.
The police are expected to release more information on the matter in due course.