Allan Young, 36, is accused of killing Michael Winn, who was left severely disabled after being shaken at five weeks old in 1998.
In 1999, Young admitted causing grievous bodily harm but, when Michael died in 2011, he was further charged with manslaughter.
Young, of Glasgow Road, Wishaw, in north Lanarkshire, Scotland, denies the charge.
During his Old Bailey trial, the jury heard that Michael's death was a direct result of the injuries he suffered years earlier which caused cerebral palsy and curvature of the spine.
His physical and intellectual development was impaired to such an extent that he had trouble breathing, was blind, incontinent and could not speak, the court was told.
Following the 1998 incident, Michael was put into care and later adopted.
On January 11 2011, his adoptive mother, Karen Heppleston-Winn, saw that Michael had stopped breathing and, despite the efforts of medics, he died overnight on January 23 2011 at the age of 12.
A post-mortem examination found he died of "respiratory insufficiency caused by pneumonia and the marked curvature of the spine" as a result of the injuries he suffered as a very young infant, prosecutor Zoe Johnson said.