The suspect, named only as Silvio S, was arrested on Thursday. The body of a child was found in his car.
It is thought to be that of Mohamed Januzi, who was kidnapped from a refugee registration centre in Berlin.
Silvio S reportedly said he had buried six-year-old Elias in an allotment.
The fate of the little boy, who disappeared without a trace from outside his home in Potsdam, had been big news in Germany.
Mohamed Januzi came to Germany with his family from Bosnia-Hercegovina more than a year ago. He was at the registration centre with his mother and siblings when he went missing on 1 October.
Police released CCTV images of a man leading the child away from the centre by the hand.
The 32-year-old suspect was arrested at his family home in the state of Brandenburg, outside Berlin, after a tip-off from his mother.
German media reports say the murders were sexually motivated.
Prosecutors in Berlin say the man suspected of murdering a four-year-old migrant boy has admitted killing another young boy, Elias, missing from his home in Potsdam since July.