Jones was born in Oswestry, Shropshire; his father, John Williams, was originally from Pwllheli, Caernarfonshire, North Wales.
[1] Jones encountered difficulties when the duke's wife, Anne Hyde, announced her intention to convert to the Catholic Church.
Further trouble ensued as Morgan wished to reunite the rectory of Llandyrnog with the bishopric of Bangor, the two positions having been held together previously.
Three years later, he wrote Some letters and papers from a late chaplain to the duke of York … touching the beginning of this plot and danger to the nation from masquerade protestants.
Jones suffered from failing sight and mental health towards the end of his life, still afflicted by the loss of his chaplaincy, and died on 8 October 1682.