In August 1605 he was one of those who disputed in moral philosophy before James I, his queen Anne of Denmark, and Henry Frederick, Prince of Wales on the occasion of their visit to Oxford.
However, on 7 April 1622, when the Spaniards were overrunning the Electorate of the Palatinate, Winniffe preached a sermon denouncing Gondomar, and comparing Spinola with the devil.
Sent to the Tower of London, Winniffe repented and appealed to the Spanish and imperial ambassadors, whose intercession caused his release a few days later.
Nonetheless, Winniffe was elected on 5 January 1642, and consecrated on 6 February; he retained the deanery of St Paul's, but resigned his livings in Essex.
[2] The outbreak of the First English Civil War disturbed his possession of his see, though according to his own account he was always at Buckden Palace and submitted to parliamentary ordinances.