The boy's mother and her partner would screw the chain into the floorboards and attach a cuff around his ankle, before going shopping in the Hildesheim area of Lower Saxony, the state prosecutor's office said on Monday.
The boy was able to go to the toilet, but the five-metre steel chain was not long enough to allow him to leave his house.
This happened at least three times by the end of 2012, the prosecutor's office said, and the boy has been in psychiatric care ever since, according to Spiegel Online.
The boy's mother and her partner said they had chained him up because they felt overwhelmed by the task of raising him.
He had, they told the prosecutor, left the house without permission and met up with fellow youngsters they did not like.
The alleged incident came to light when the boy told his biological father what had happened.
The 41-year-old mother her 48-year-old partner face charges of abuse and imprisonment.
A court date is yet to be fixed.