Shohfah-El Israel, 40, from Cricklewood, North London, is on trial at Reading Crown Court for the alleged murder of Joy Morgan.
The jury has heard that Ms Morgan has not been seen or heard from since attending a United in Christ church celebration dinner on Boxing Day last year.
Giving evidence on Tuesday, Israel admitted that he had allowed an "upset" Ms Morgan to stay at his Cricklewood home after the event.
The pair watched videos, ate dinner out and discussed issues affecting their church on December 27 and 28, the jury heard.
Israel said that during their conversations, Ms Morgan revealed she was "leaving the church" that he said had been hit by "controversy".
He explained that after the church dinner, the plan had been to leave Ms Morgan with his wife at their home in Luton, before he went to stay at his other home in Cricklewood.
Israel described the student as "100% part of the family" who was like a "daughter" and frequently stayed at both properties.
But on December 26, Ms Morgan asked to be taken to her accommodation in Hatfield instead, Israel told the court.
He said he drove her there and on arrival she started "crying" and said she was "leaving".
Ms Morgan, who was 20 years old when she disappeared, asked to stay at Cricklewood instead, but Israel said it was not a good idea.
"I was already breaking the rule by dropping her off," he told the court.
"If [church] leadership heard about it, it's going to be hell."
The court has already heard that the United in Christ church had strict rules on relations between men and women.
Ms Morgan, as a single female, could not have travelled alone in the car with Israel according to church rules, the jury was told
But Israel said he allowed her to stay at Cricklewood that night because she was "upset".
She slept on a sofa bed, he told the court, for two nights without his wife knowing.
Asked by his counsel Ed Brown QC, why he did not initially tell his wife when she rang him, Israel said: "My wife is not very tolerable of people wanting to leave the church or saying things about the church."
On December 27, Israel said he worked on his PC while Ms Morgan was out, and later the pair watched YouTube videos and had dinner on Kilburn High Road.
He allowed her to stay another night because she told him she wasn't "stressed" and "felt alright" in Cricklewood.
On December 28, a Friday, he said Ms Morgan was out in the morning, before the two prepared for the Sabbath the next day.
He said he drove her back to Hatfield that night.
The court previously heard Israel initially told police he dropped Ms Morgan off at Hatfield on December 26, before saying she had in fact stayed at his flat for two days.
The jury was also previously told calls were made from Ms Morgan's phone to the NHS Direct 111 service on the evening of December 28 but a transcript showed no words were spoken.
Asked by Mr Brown on Tuesday if he had heard or made those calls, Israel said he had not.
He told the court Ms Morgan discussed with him a video made by a US member of the church that criticised a bishop's business dealings.
Ms Morgan claimed to have "inside information of people who were planning on leaving", Israel told the court.
He said that "hundreds" of people were breaking off from the church towards the end of 2018.
"People would leave and join people who had already left and start saying malicious things about the church," he explained.
YouTube videos were being circulated by ex-members criticising how the church was run, the jury was told.
Israel said one church member, named Judah Mac, was demoted and left.
"Some people were against that, saying that the way they were treated, the way they were demoted wasn't right," Israel said.
The court heard how the church, based in the US, had a male hierarchy of bishops, deacons, officers, soldiers, brothers, with women just named as sisters.
Israel himself was demoted in front of the congregation over interrupting another church member who was speaking to some women.
He said male church-goers were warned they should always have someone with them when they were with the sisters in case some made "false" accusations.
Earlier in the trial the jury was told that after Israel was arrested the keys to Ms Morgan's Hatfield accommodation were found in the passenger footwell of his car.
Israel told the court on Tuesday that the only time he previously spent alone with Ms Morgan was when giving her lifts in his car.
He said he and his wife had advised Ms Morgan to get spare keys and he gave her a key-chain.
But he added: "I honestly don't remember or recall her ever giving me the keys."
Earlier on Tuesday, the court heard that Israel, originally from Nigeria, occasionally took more than his prescribed dosage of medicine to cope with long-standing health problems affecting how he walked.
He married his wife Chindu Israel in 2016, against her family's wishes, whose alleged actions, including leaving a sacrificed pigeon at their home, led the couple to move several times.
Israel denies killing Ms Morgan between December 26 and December 30 2018. He is due to continue giving evidence from 10am on Wednesday.
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