The teenager was arrested at an asylum shelter in the western city of Cologne in September, with the authorities describing him as a "serious threat".
Police at the time said the suspect's mobile phone showed he had been in touch with an Isis contact abroad and had expressed willingness to carry out an attack.
Investigators found online chat messages on the phone that included "concrete instructions" for building an explosive device, prosecutors added.
Officers searching his accommodation discovered a battery pack, 70 sewing needles and several butane gas cartridges - items that could be used to prepare a bomb, DPA national news agency reported, citing the charge sheet.
The trial at the district court in Cologne, scheduled to last until March 20th, is being held behind closed doors because the accused is a legal minor.
A court spokesman said he had to answer charges of planning "a serious act of violence threatening state security".
If convicted, he faces a maximum sentence of five years' detention under the juvenile penal code.
The teenager and his family were among the nearly 900,000 migrants and refugees who arrived in Germany in 2015, a record influx that has fuelled security concerns.
The teen was brought to police attention after residents and employees at the refugee shelter where he was staying voiced concerns that he had been radicalised, as did a local mosque.
Germany is on high alert following a series of attacks claimed by Isis, the deadliest of which was a truck rampage through a Berlin Christmas market which killed 12 people in December.