John Westland, 28, pleaded not guilty to the murder of Liam Deane when he appeared before Leeds Crown Court.
Deane, 22, died at the prison on November 12 this year, five weeks after he was sentenced for the murder of his baby daughter.
Westland appeared in court via a video link from Wakefield Prison.
Westland spoke only to confirm his name, date of birth and nationality before entering the not guilty plea.
A trial date was set for July 23 next year and is expected to last one week.
Police confirmed Deane had been found dead in his cell at the prison.
Deane was given a life sentence with a minimum of ten years on October 5 after admitting to killing two-day old daughter Luna at his family home in Wakefield.
Leeds Crown Court heard baby Luna had been left in the arms of Deane while her mum went to get some sleep on July 10.
Deane lost his temper during the night and subjected Luna to an attack when she continued to cry.
He admitted punching Luna to the face, squeezing her body and arms and shaking her.
Luna was taken to Leeds General Infirmary where she died in intensive care on July 14.
A doctor concluded Luna had died after suffering head trauma, leaving her with “catastrophic brain injuries.”
Deane broke down when interviewed by police and admitted that he was responsible for attacking the baby.