In 2006, Williams received the honorary degree of Doctor of Divinity from the University of Wales in recognition of his contribution to biblical scholarship and to religion and education in Wales. In 2011 the volume "The Bible in Church, Academy, and Culture: Essays in Honour of the Reverend Dr. John Tudno Williams" edited by Alan P. F. Sell was published in honour of his contributions to the Church and to scholarship. In 2012 he was elected a Fellow of the Learned Society of Wales.