The 38-year-old, who has not been named, told customs officials after being detained with a forged visa on Thursday that he intended to use the precious stone to buy cars in Portugal. He also said the stone was worth just €50,000.
But an examination concluded the diamond, around three centimetres high and three centimetres wide, was worth around €2.5 million.
The man, who was unable to produce documentation for the precious jewel, is accused of "a whole range of offences" including breaching international rules meant to stop the trade of "blood diamonds" from conflict areas, customs spokesman Hans-Jürgen Schmidt said.
He also faces charges of smuggling and of withholding around €500,000 in import taxes, and was due to go before an investigating judge late on Friday, Schmidt told AFP.
"The diamond will most likely be confiscated and go to the German state," Schmidt said. "He will not be a free man whatever happens. The judge will either remand him in custody or he will be deported to Angola."