Vikki Thompson, 21, was found dead in her cell at HMP Leeds in 2015 with a ligature around her neck.
Robert Steele told the hearing in Wakefield Miss Thompson wrote to him while in prison saying: "I know I'm going to do something silly."
Giving evidence he said: "I believe she shouldn't have been in a male prison."
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The jury inquest was also told Miss Thompson, from Keighley, had repeatedly told prison and court escort staff that she would be "carried out in a box".
Mr Steele said he spoke to her on the phone while she was in prison and she told him she wanted to move to a women's prison that and her solicitors were waiting for her to make a formal application to the governor.
Mr Steele also said he received a letter from his partner which said: "I don't think I can last very long in here. I can't sleep at night. I just feel like I won't be here no more.
"I know I'm going to do something silly. I don't want to but I can't do this."
But, in a statement read to the court, Miss Thompson's mother Lisa Harrison said her daughter did not say she had a problem being in a men's prison.
"Vikki didn't like prison but who does?" Ms Harrison said. "She never said anything to me about it being the wrong prison for her."
The inquest heard Miss Thompson had identified as female since she was 10 years old but had never had any surgical or hormone treatment.
She did not have a Gender Recognition Certificate establishing her female identity so she was sent to a men's prison.
Coroner Jonathan Leach said the inquest would examine a number of issues including the suitability of the "prison accommodation".
The jury was told that after an extensive risk assessment process Miss Thompson was initially put in E-Wing rather than A-Wing, where vulnerable prisoners were housed, and placed on a one-hour suicide watch.
Mr Leach said this decision was taken because it was thought she might be under more risk on A-Wing due to the number of sex offenders there.
He said she was later allowed to move to A-Wing but was taunted by men in the segregation block below.
The inquest heard that on the day she died Miss Thompson had been seen watching TV at 19:00 GMT but at 20:00 she was spotted on the floor with the ligature round her neck and the alarm was raised.
The inquest, which is expected to last three weeks, continues
The partner of a transgender woman found dead in a men's prison while on remand has told an inquest she did not want to be in a male jail.