Detectives have been investigating him for alleged offences relating to his teachings which they had termed offensive and against the law.
The prosecution said they had reasons to believe there were criminal activities of indoctrination being carried out at Wekesa's church.
He was arrested on Thursday last week and questioned by sleuths from the Directorate of Criminal Investigations (DCI) for two days.
The police had accused him of running a religious cult similar to Pastor Paul Makenzi's in Shakahola, Kilifi County, where over 200 people died after starving to death in the name of fasting in order to meet 'Jesus Christ'. Over 200 bodies have been exhumed from the forest with fears that there are more after families continue to report missing relatives.
Lawyer George Wajackoya (left) was among those representing 'Yesu wa Tongaren' in court. [Juliet Omelo, Standard]
The police had accused Wekesa of engaging in cultism in Tongaren, claiming to be Jesus Christ. The officers said he had been teaching radical ideologies to his followers while engaging in money laundering, accusations that have all been dropped.
Wajakoya noted that every religious leader has a right to preach the word of God and is protected by the Constitution.
The prosecution had also said they had reasons to believe there were criminal activities of indoctrination being carried out at Wekesa's church.
Last Friday, the court granted the prosecution four days to hold the suspect so they can complete their investigations. However, the investigators found nothing incriminating against him.
Wekesa's lawyer George Wajackoya condemned the arrest of 'Yesu wa Tongaren' saying it was politically instigated by leaders from Bungoma County.
"It is very wrong to incriminate a religious leader based on the Shakahola incident. This man is very innocent and his arrest was purely political. A lot of Bungoma leaders, including the governor, were on the forefront pushing for his arrest," Wajackoya told the court.
Wajakoya further noted that every religious leader has a right to preach the word of God and is protected by the Constitution.
The principal magistrate ruled that Wekesa had no case to answer after the prosecution failed to adduce any evidence before the court to enable his prosecution.
"The suspect has not been found with any offence following investigations that were done by police and therefore is set him free," ruled Mr Orlando.
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Wekesa thanked the court for setting him free saying; "It is God's doing".
"I had earlier on said my lawyers would be the sun and the moon but God came through and placed a rainbow on my side in the form of lawyer Simiyu Wamalwa who has stood with me since the beginning, and Prof Wajackoya who has come today to stand with me. I don't take it for granted," said Mr Wekesa
Wekesa noted that he is not like other men of God who thrive in wealth but instead leads a simple and truthful life, preaching the word of God.
"On Saturday, I went with some police officers to my home during their investigations, and I was glad, being a sabbath day, they got a chance to witness and count the offerings that were collected; Sh250, six tomatoes and four onions," said Wekesa.
Wekesa told the court that his only wealth is his beard and the hair on his head.