The girl's mother has admitted allowing the death
A malnourished and dehydrated toddler died after her back was "snapped in two" by her father, a court has heard.
James Howson, 25, denies murdering 16-month-old Amy at the family house in Edlington, Doncaster, South Yorkshire. He also denies two counts of cruelty.
It is alleged Mr Howson held his daughter over his knee and hit her so hard it broke her back, a jury at Leeds Crown Court heard.
His partner Tina Hunt, 26, has admitted allowing the death of a child.
Opening the trial, prosecutor Gary Burrell said the toddler was covered in fractures and bruises from a number of assaults.
He told the court Amy had been "slapped and punched" in the months leading up to her death.
On 23 December, 2007, paramedics were called to Nelson Road and arrived to find the child naked apart from a nappy on a sheet in the doorway to the living room.
Mr Howson was trying to resuscitate the child and both parents were crying.
Amy was taken to Doncaster Royal Infirmary, but died less than an hour later.
The court was told Mr Howson had been looking after his daughter because her mother - his partner Tina Hunt - who at the time was 12 weeks pregnant, had morning sickness.
He told police and paramedics Amy had fallen out of bed and hit her head. He said he fell asleep with the child in his arms and woke to find her unconscious.
The jury was told Mr Howson had blamed her other injuries on the family's pet dog, a Staffordshire bull terrier, and other incidents around the home.
Mr Burrell said: "The nature and extent of the injuries themselves indicate the child must have been in extreme pain and in poor physical condition for a period of weeks prior to death."
Pathologists gave the cause of death as the spinal injury along with a serious head injury.
Amy was also found to be "seriously under-nourished and dehydrated".
The court was told in interview, Mr Howson told police he was "unaware" of the child's injuries.
Mr Burrell said it was "inconceivable" that anyone looking after the child would not have been aware of her pain and distress.
The trial continues.