The body of Elisabeth-Jane Ross, 38, was discovered by a homeless man in a derelict building in the Kypseli area of the Greek capital on 18 July.
The authorities are yet to publicly confirmed the suspect’s identity.
He arrived at court for a hearing on Wednesday morning in an unmarked grey Hyundai i30 car, alongside a number of police officers.
The court is located on the city’s Evelpidon Street, just a few minutes’ walk from where the charity worker’s body was found.
The man, who was initially detained on illegal weapons possession charges, is facing a murder charge as well as accusations that he stole more than €10,000 (£8,573) from the victim’s bank accounts using her bank cards, police said.
Greek officials said he admitted moving the body but has denied the murder allegations.
Police said the suspect was detained for questioning after investigators reviewed surveillance camera footage recorded near the abandoned building.
After allegedly murdering Ms Ross, who is understood to be from Edinburgh in Scotland, the man is accused of sending a series of messages from her phone to her friends and family before switching off the device.
He is then said to have bought another phone and texted her friends in Athens, including his wife, impersonating an unnamed jihadist saying he had killed the Scot because of her religion, Greek newspapers Proto Thema and Ta Nea reported.
The newspapers reported that his wife told the police that she suspected her husband’s involvement in the murder when she woke up to find he was not in their apartment and tracked his phone to where Ms Ross was staying.
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Ms Ross is believed to have died between five and seven days before she was found, during a heatwave in which temperatures reached 36C.
The Hellenic Police, Greece’s national force, were able to identify her using fingerprints and with the help of Interpol.
Ms Ross entered Greece on 26 June and was initially staying with friends in Piraeus, a port area of Athens.
She is then said to have gone to meet American friends in another part of the city, but it is unclear if this ever happened.
Authorities are awaiting the results of tissue analysis to determine whether she died from suffocation, as suggested by a preliminary assessment by the medical examiner.
The Foreign, Commonwealth and Development Office (FCDO) said earlier: “Our thoughts are with Elisabeth’s family during this difficult time.
“We are providing consular support and are in contact with the local authorities.”
Police Scotland is also liaising with authorities in Greece and is providing support to Ms Ross’ family.
