Michael Plumadore is charged with killing Aliahna Lemmon. Her remains were recovered Monday evening.
The girl and her two sisters had stayed with Plumadore for about a week while their mother was ill.
Plumadore told police he last saw Lemmon sleeping in his home early Friday morning. He said he noticed she was missing a short time later and assumed she went back home to her mother.
Because of a lack of communication, Lemmon was not reported missing until Friday night.
Allen County Sheriff Ken Fries told Fort Wayne television station WISE-TV there was not a specific location where the girl's remains were found, but in a press release Corporal Tinkel says her remains have been located and recovered.
Plumadore has been placed on a 72-hour hold. A pretrial hearing has been scheduled for Dec. 30 at 9 a.m. No bond has been set.