A post mortem revealed the man, in his 50s, had suffered serious head injuries, suggesting murder.
"We're assuming he was murdered in September 2000," said Christiane Leven, police spokeswoman in the northern city of Hamburg. Police have arrested a 30-year-old careworker who used to look after the wheelchair-bound man.
Police discovered the remains of the corpse Thursday after breaking into the man's apartment when neighbors complained of a strange smell.
Germany often reports cases of people lying dead in their homes for months or years before discovery, a phenomenon sociologists attribute to mounting social isolation and the disintegration of the family.
The efficient banking system also means people's bills and pensions can continue to be paid long after they die.