Andrew William Campbell was accused of murder when arrested more then three years ago but is set to have the charge downgraded to one of manslaughter.
Paramedics found the body of Dexter Wilton inside a property at Raceview in Ipswich on June 21, 2019.
Medical evidence found he died of dehydration and malnutrition, with prosecutors saying evidence suggested he was left alone without food and water for at least 21 hours before he died, a court has been told previously.
Dexter's mother Natalie Jade Whitehead was charged about 18 months later with murder and interfering with a corpse over the baby's death.
Campbell allegedly lived in the Ipswich house when the child died.
He and Whitehead had been in a relationship for at least four weeks at the time Dexter died, the court heard earlier.
They were no longer together when both were arrested.
Whitehead's version of events is that she put the child down about 8.30pm and did not check on him until 5pm the next day, earlier proceedings have heard.
The Crown has alleged the couple were on a three-day drug binge in the days before the baby died.
The Crown did not oppose Campbell's bail application in the Brisbane Supreme Court on Friday, saying the murder charge he is facing will be substituted for one of manslaughter.
There was a risk Campbell could spend too much time in custody as it was likely the case would only go to trial in 2025, Justice Catherine Muir said.
The 42-year-old is to live with his parents and consented to wearing an ankle GPS monitor.
Campbell's matter is listed for mention in Ipswich Magistrates Court on July 21.
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