The man, identified only as Yve M, is accused of using a knife to stab his girlfriend 30 times before beheading her corpse.
He then cut off her left arm and the little finger on her right hand before decorating her body.
When police found the victim, identified by police as Tunay G, her body had already begun decaying.
Bizarrely, the woman’s body had also been decorated with stones, feathers and string – leading investigators to suspect a ritual killing.
The brutal killing took place sometime on May 15 or May 16 last year. The suspect, also aged 39, was arrested on June 11.
The pair met in 2015 when they were both living in temporary accommodation. They then moved in together in the Berlin neighbourhood of Mariendorf a month before the attack.