BATON ROUGE - The mother of a 2-year-old who was found dead over the weekend is now charged in the toddler's death. Police have also upgraded charges against her boyfriend.

Just an hour before BRPD held a news conference to discuss new developments in the death of Nevaeh Allen, officers at a State Police facility were seen placing the girl's mother, Lanaya Cardwell, in the back of a police unit in handcuffs. Police confirmed at that briefing Wednesday that Cardwell was charged with second-degree murder.

Read more: Mother of slain toddler held on $300K bond

Arrest documents said the 2-year-old picked up her mother's contact lenses as she was getting ready for work that morning. Cardwell allegedly punched the toddler, causing her to fall backward and hit her head on a cabinet. 

The mother's live-in boyfriend, Phillip Gardner, told police Cardwell grabbed Nevaeh and took her into another room. He described hearing "what sounded like two adults fighting in the room," according to arrest documents. 

Gardner added that Nevaeh had a bruise on her forehead when he left to take Cardwell to work. He said when he got back, the toddler laid down on the couch, refused to eat because of stomach pain and became unresponsive.

Arrest documents say Gardner tried to revive her using CPR but was unsuccessful. He told police he left his phone at the apartment and put the toddler in a small suitcase. He drove the other two children to Mississippi, where he buried Nevaeh in the woods and threw her clothes in a trash can. 

Along with Neveah, Gardner was also watching a 3-year-old and an 11-month-old at the time. 

An autopsy report said Nevaeh had multiple bruises on her face and head, along with swelling in her brain. The coroner noted that the marks on her face resembled handprints. There were also bruises on her thighs and rear. Injuries to her abdomen were consistent with being punched in the stomach. Because Nevaeh had severe brain trauma, the coroner said it was possible Nevaeh was still alive when Gardner placed her in the suitcase and suffocated to death.

WATCH: Nevaeh Allen's mother taken away in handcuffs

The toddler was found dead in Mississippi on Sunday, two days after Gardner reported her missing from the apartment complex on La Belle Avenue in Baton Rouge. 

Gardner initially told investigators that Nevaeh disappeared after he fell asleep Friday afternoon, kicking off a days-long search for the child involving State Police and the FBI.

Gardner later changed his story, telling investigators he found the girl unresponsive and then disposed of her body. He later led officers to a wooded area where they found the child's remains.

He too is charged with second-degree murder, along with obstruction of justice and unlawful disposal of remains. 

Gardner told police he could not explain why he did not call 911 when he realized Nevaeh needed medical attention. He said he had seen previous instances of Cardwell being abusive, but never intervened or reported it.