Students have spoken out about the captivity they allegedly endured at the Midwest Academy in Keokuk, a city along the Mississippi River.
The students claims they were sometimes locked in the boxes for days or weeks at a time and wouldn't be let out unless they sat in a specific posture for 24 hours.
According to the Associated Press, students who attended the school between 2008 and September 2015 described dark, cell-like punishment rooms that were filled with sounds of students' screams, mixed with motivational recordings.
It is alleged staff supervised the students by watching them on a surveillance camera.
"You can't sleep because there is a lot of noise. A lot of girls like to scream in there," she said.
"You basically look forward to bathroom breaks and those moments when you can get out of your box."
It's a brutal punishment you probably wouldn't even expect in prison and Ms Beaman began cutting herself with a bottle cap and begged emergency services to place her elsewhere, after she was isolated for weeks.
She even attempted to escape but failed.
Lauren Snyder, 17, told AP she begged to get out of isolation last year after a staff member allegedly tortured her by turning up a recording so loud that it blew out the speakers, making a screeching sound.
"It was complete hell," she said.
After being released she went to a psychiatric hospital after attempting to kill herself with a sock.
Sarah Wilson was locked in isolation when she didn't take her belly button ring out.
She told AP she knew she would lose her mind in there.
Ex-student Shaun McCarthy, 19, considered himself lucky he only had to go into isolation twice.
"That is the worst I've ever been treated," he told AP.
"It's not humane."
It was also alleged students only got to eat small meals while they were in isolation and had no stimulation.
Mr McCarthy told AP it could get even worse and he once had to help staff watch the boxes.
He said he once saw a girl puncture her finger and write on the walls with blood.
He also witness a girl urinating on the floor in the room.
Writing long essays or sitting in a certain position for 24 hours were allegedly the only ways out.
Former student Rachel Adkisson, 19, told the FBI that she knew a girl who tried to commit suicide with a bra strap.
Ms Adkisson had also been put in isolation for refusing to run during a sport lesson.
AP reports she had lost nine kilograms when she was released from isolation after two weeks.
"It's like torture," she said.
"You think it's never going to end. You think, how can a human do this to another person?"
The Midwest Academy claims to be a therapeutic boarding school that provides struggling teens with a "safe, structured and disciplined" environment.
According to the school's website, it teaches students accountability, responsibility, teamwork, integrity and self-awareness.
The teachings cost parents about $5000 a month and academy owner Ben Trane said students were fortunate to have its staff in their lives.
Some parents have even left glowing reviews about the school on its Facebook page.
"Midwest Academy has saved many children's lives as well as taught them solid principles to live by," one mother said.
"My experience with them ended in 2006, but the staff was always professional and caring."
Before the ex-students spoke out, the school was raided by officers January 28 over other allegations that a staff member sexually assaulted a student.
Those allegations have now expanded into an investigation into other possible criminal activity and abuse.
Another mother wrote on Facebook that the school saved her son's life.
"He was headed to prison or suicide," she said.
"He is now doing great ... great self esteem, good job. etc.
"I called him tonite (sic) and asked him if he witnessed or heard anything like what they are saying happened and he said 'absolutely not'."
Mr Trane would not respond to AP's interview requests.
The school has since been temporarily closed and some students have already spoken with the FBI.
Juvenile law expert and university professor, Jerry Foxhoven, told AP long-term isolation could be damaging for teens and worsen mental health issues or contribute to post-traumatic stress disorder.
He said parents wouldn't be allowed to keep children in isolation for weeks without facing abuse allegations, and the academy shouldn't either.
AP understands parents were "in the dark" about the alleged abuse because the school strictly limited and monitored communication.
Where to get help:
• Lifeline: 0800 543 354 (available 24/7)
• Suicide Crisis Helpline: 0508 828 865 (0508 TAUTOKO) (available 24/7)
• Youth services: (06) 3555 906
• Youthline: 0800 376 633
• Kidsline: 0800 543 754 (available 24/7)
• Whatsup: 0800 942 8787 (1pm to 11pm)
• The Word
• Depression helpline: 0800 111 757 (available 24/7)
• Rainbow Youth: (09) 376 4155
• CASPER Suicide Prevention
If it is an emergency and you feel like you or someone else is at risk, call 111.