As dean of Windsor he assisted at the christening of Edward VI and the funeral of Lady Jane Dudley, and his signature is affixed to the decree declaring the invalidity of the marriage of Henry VIII with Anne of Cleves. On 14 January 1545 he surrendered to the crown his hospital of Kepyer and most of his benefices, and he also alienated the revenues of his deanery, some temporarily, others in perpetuity. The complaints against him on this score were so loud that after the accession of Edward VI he was compelled to resign. He retired to Chalfont St. Giles, where he died in January 1556, and was buried in the church. His will met with disapproval, for a grant was made to one J. Glynne of so much as he could recover of goods, chattels, and money, devised by Franklyn for superstitious purposes. A large number of letters addressed by Franklyn to Wolsey, Thomas Cromwell, and others were preserved, in the Public Record Office and the British Museum.