During the ten years 1603-13 Gordon produced a number of quartos notable for obscure learning, Protestant fervour, controversial elegiacs, and prophetic anticipations drawn from the wildest etymologies. He was assiduous in his ecclesiastical duties, which included a quasi-episcopal supervision of some eighty parishes. He procured an act of the chapter devoting one-fifth of the revenue of every prebend for seven years to cathedral repairs. While on a triennial visitation he died at Lewston House, Dorset, in his seventy-fifth year. He was buried on 6 September in the morning chapel of his cathedral, where an inscribed stone marks his grave.