Daniel Rigby, 23, from Tyldesley, Wigan, was found guilty of murdering his girlfriend's son by a jury of six men and six women.
Rio's mother Kirsty Smedley, 24, formerly of Cheriton Drive, Breightmet, Bolton, was also found guilty of allowing or causing the death of a child.
The prosecution said she failed to protect her son from Rigby, a man she had previously reported to police for violently attacking her while she was pregnant.
Rio was murdered by Rigby on April 22 in what the prosecution said was "a wicked attack on a defenceless two-year-old child".
Rio Smedley had 91 separate injuries on his body and died from a ruptured liver, a trial at Manchester Crown Court heard.
Daniel Rigby, 23, of no fixed abode, has been found guilty of the murder of two-year old Rio Smedley, the child of his then partner Kirsty Smedley.
Ms Smedley has also been found guilty of allowing his death.
Rigby had denied murdering Rio Smedley, who died on 22 April from a ruptured liver and had 91 separate marks of injury on his body.