Baker's boyfriend, Michael Scott, also faces first-degree murder charges in Bryeon's death. Both were charged on Saturday.
Bryeon, 1, was reported missing on Tuesday. Baker told police three men attacked her and took off with the boy, prompting an Amber Alert. But prosecutors say Baker and Scott beat the boy when he wouldn't stop crying, and dumped his body.
Police have searched areas near the Des Plaines River, but the boy's body has not been found.
Baker is being held without bond. Scott is being held on $750,000. Baker's lawyers say she is not guilty.