Rosdeep Adekoya, 34, appeared before judge Lord Boyd at the High Court in Edinburgh yesterday.
The Crown allege she murdered her three-year-old son after assaulting him on various occasions between January 12 and January 15, 2014.
Prosecutors also claim she attempted to defeat the ends of justice by telling lies to police officers who were investigating her child's disappearance.
Ms Adekoya, whose address was given as being a prisoner of Cornton Vale in Stirlingshire, did not enter a plea during the two-minute long hearing.
Prosecution lawyer Alex Prentice QC told the court there had been discussions between the Crown and Ms Adekoya's legal representatives.
Mr Prentice said these discussions were ongoing and asked for the case to be continued to a hearing later this month.
Ms Adekoya's defence advocate Brian McConnachie told the court he would not be entering a plea at this stage on his client's behalf.
Ms Adekoya, originally of Drylaw, Edinburgh, was arrested by police following claims her child disappeared from her home in the city last January.
Hundreds of members of the local community helped police search for Mikaeel in the days before his body was discovered in woodland behind a house in Fife.
According to a legal document that has been placed before the court, prosecutors allege that on various occasions between January 12 and January 15, 2014 at a flat in Ferry Gait Crescent, Edinburgh, Ms Adekoya assaulted her son by repeatedly seizing hold of him and punching him on the head and body.
It is claimed her actions caused his body to strike against a hard object and she inflicted blunt force injuries on his head and body. Prosecutors also claim she failed to seek medical attention for him and that she murdered him.
The second charge alleges that between January 14 and January 17, 2014, at the Ferry Gait Crescent, Edinburgh, address and an area of woodland behind a house at Dunvegan Avenue, Kirkcaldy, Fife, and at Drylaw police station in Edinburgh, Ms Adekoya attempted to defeat the ends of justice.
Prosecutors allege she did this in a bid to avoid being detected, arrested and prosecuted for the crime.
It is alleged she wrapped the dead body of Mikaeel in a duvet cover before placing his dead body in a suitcase and transporting the suitcase in a car.
Prosecutors claim she transported Mikaeel's remains from the Ferry Gait Crescent address via Flora Stevenson Primary School, Comely Bank Road, Edinburgh, to an area near Dunvegan Avenue, Kirkcaldy.
The case against Ms Adekoya will next call at the High Court in Edinburgh on July 25.