In 1478 he spent some weeks in prison, apparently as a result of some association with the disgraced George, Duke of Clarence. He was imprisoned again in 1485, shortly after Henry VII's victory at Bosworth. Some say this was due to Stillington's involvement in the matter of Edward IV's bigamy, for the new king needed to reverse the bigamy charges that made his future queen, Elizabeth of York, illegitimate.
Some years after his second release, Stillington became involved in the plot to place the impostor Lambert Simnel on the throne (1487). He was imprisoned a third time, and died in prison.