Maldonado, also known as Daniel al-Jughaifi, was captured by the Kenyan military as he tried to flee Ethiopian and Somalian forces on 21 January, DeGabrielle said.
He was turned over to US officials this weekend, flown back to Houston and on Tuesday went before magistrate Calvin Botley, who ordered him to be held without bail until a February 20 detention hearing.
First case from Somalia
"This case represents the first criminal prosecution of an American suspected of joining forces with Islamic extremist fighters in Somalia," said Kenneth Wainstein, US assistant attorney general, in the same statement.
It "serves as a warning to others who would travel overseas to wage violent jihad," he said.
In Somalia, Maldonado got an AK-47 rifle, military combat uniform and boots, and training in fitness, firearms and explosives, the statement said.
He is charged with conspiring to use a destructive device, which carries a maximum sentence of life in prison, and receiving military training from a terrorist organisation, with a maximum punishment of 10 years behind bars.
Ethiopian forces backing the Somalian interim government ousted Islamic forces from the capital Mogadishu in a December offensive.
The US has launched at least one air strike against suspected al-Qaeda forces in Somalia since then and there have been unconfirmed rumours that US forces are on the ground in the unstable Horn of Africa country.