The body of Kaydence Mills was found at the Chinchilla Weir, about 300km west of Brisbane, in March 2020.
Detectives uncovered the remains days after charging Kaydence's mother Sinitta Dawita, then aged 28, with her murder.
Dawita's fiance Tane Desatge, then aged 40, was also charged with murder.
The pair are each also charged with interfering with a corpse and torture.
Desatge earlier this year had applied to be granted a judge-only trial on the basis that jury members would be prejudiced by hearing testimony that could only be used against one defendant.
Supreme Court Justice Martin Burns in Brisbane on Wednesday granted the application, finding that jury members would be unlikely to disregard some of what they heard about in a case involving "highly emotive" allegations.
"The cumulative effect of the evidence will probably inflame or at least distract the jury from the issues at trial," Justice Burns said.
Kaydence was born in September 2014, but had not been seen since 2016.
The charges stemmed from a police investigation that began in November 2019 into what happened to the little girl.
Crown prosecutor Michael Lehane had opposed the application and submitted that a jury could be directed against misusing evidence against one defendant when deliberating about another.
Justice Burns said his belief that a jury not follow such a direction had been fortified by a "bewildering" news story published by the Toowoomba Chronicle newspaper in June.
"There is, in my view, a high risk that the article was read by one or more prospective jurors. Especially so given what must be regarded as a prominent case," Justice Burns said.
Justice Burns scheduled Dawita and Desatge to face a joint trial to last three weeks starting on July 22.
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