After a trial lasting more than a year, the district court in Hanau, Hesse, acquitted the accused mother of the boy in another trial about the murder of a four-year-old boy 34 years ago.
The decision was made due to a lack of evidence, a court spokeswoman said on Tuesday.
The prosecutor's allegations have not been proven.
She had accused the 61-year-old of killing her physically and mentally neglected son.
The boy is said to have choked on his vomit on August 17, 1988 in a sack tied over his head.
The public prosecutor had accused the woman of putting her son in the sack, tying it up and placing the child in the care of the alleged cult leader.
The 75-year-old wanted the boy's life.
Presumably she wanted to maintain and strengthen her leadership in the sect.
Her mother had convinced her that the four-year-old was the "reincarnation of Hitler, a power sadist and obsessed with the dark" and was being taken by God.
She left the boy in the sack to himself, although she is said to have heard his panicked screams.
The mother accepted the death of her child with approval.
With the verdict, the judges followed the plea of the defense.
Prosecutors had asked for life imprisonment.
The reason given by the chamber was that it could not be determined with the necessary certainty that the accused tied the bag shut.
An alternative course of events is possible.
So it is conceivable that the sect leader tied the sack over the child's head.
The mother also knew nothing about a possible act by the leader.
Therefore, a jointly committed murder is not proven.
The presiding judge said on Tuesday that the 61-year-old should be compensated for the deprivation of liberty she suffered.
In September 2020, the Hanau Regional Court had already sentenced the cult leader to life imprisonment for murder.
The mother was arrested the day after the verdict was announced and has been in custody ever since.
However, the Federal Court of Justice overturned the judgment against the sect leader in May 2022 due to a legal error and referred the proceedings to Frankfurt am Main.
The Karlsruhe judges criticized the fact that the regional court had not dealt in detail with whether the case concerned a killing through active action or through omission.
In addition, the culpability of the woman must be checked again.
The entire case only came to light after many years of media research.
ala/dpa
