Cedd had been brought up in the Celtic Rite which differed from the Roman Rite, both in the accepted form of the tonsure (i.e. the shaven patch of scalp adopted by Christian monks) and in the method of calculating the date of Easter. These differences came to a head within the Northumbrian kingdom at a meeting known as the Synod of Whitby. The proceedings of the council were hampered by the participants' mutual incomprehension of each other's languages, which probably included Gaelic, Old English, Frankish and Early Welsh, as well as Latin. Bede tells us that Cedd was a conscientious interpreter for both sides. Cedd's facility with the languages, together with his status as a trusted royal emissary, must have given him a key role as a go-between in the negotiations. When the council ended, he returned to Essex. According to Bede, he accepted the Roman observance of Easter,[7] and returned to his work as bishop, abandoning the practices of the Scots - by which Bede means the Irish from the Kingdom of Dál Riata.

A short time later, he travelled back to Northumbria, this time to the monastery at Lastingham, where he fell ill with the plague and died on October 26, 664. Bede records that a party of thirty monks travelled up from Essex to Lastingham. All but one small boy died there of the plague. Cedd was initially buried at Lastingham in an open-air grave, but his body was moved to a shrine inside the later stone church at the monastery. Chad succeeded Cedd as abbot at Lastingham.

King Swithelm died at about the same time as Cedd and was succeeded by the joint kings Sighere and Sebbi. There was a partial reversion to paganism, which Bede blames on the effects of the plague. Mercia under King Wulfhere was now the dominant force south of the Humber, so it fell to Wulfhere to take prompt action. He dispatched Bishop Jaruman to take over Cedd's work among the East Saxons. Jaruman, working (according to Bede) with great discretion, toured Essex, negotiated with local magnates, and soon restored the situation.