William had adopted a policy of conciliation towards the church after the first rebellions broke out in late 1067, giving Stigand a place at court, as well as giving administrative positions to Ealdred of York and Æthelwig, Abbot of Evesham.

Archbishop Stigand appears on a number of royal charters in 1069, along with both Norman and English leaders.

He even consecrated Remigius de Fécamp in 1067 as Bishop of Dorcester.

Once the danger of rebellion is past, however, William has no further need of Stigand.

At a council held at Winchester at Easter 1070, the bishops meet with papal legates from Alexander II.

Stigand is deposed on April 11, 1070, by the papal legate, Ermenfrid, Bishop of Sion in the Alps, and is imprisoned at Winchester.

His brother Æthelmær, Bishop of Elmham, is also deposed at the same council.

Shortly afterwards, Aethelric the Bishop of Selsey, Ethelwin the Bishop of Durham and Leofwin Bishop of Lichfield, who is married, sre deposed at a council held at Windsor.

There are three reasons given for Stigand's deposition: that he held the bishopric of Winchester in plurality with Canterbury; that he not only occupied Canterbury after Robert of Jumièges fled but also seized Robert's pallium which was left behind; and that he received his own pallium from Benedict X, an antipope.

Some accounts state that Stigand did appear at the council which deposed him, but nothing is recorded of any defense that he attempted.

The charges against his brother are nowhere stated, leading to a belief that the depositions were mainly political.

That spring he had deposited his personal wealth at Ely Abbey for safekeeping, but King William confiscates it after his deposition, along with his estates.

The king appoints Lanfranc, a native of Italy and a scholar and abbot in Normandy, as the new archbishop.

King William appears to have left the initiative for Stigand's deposition to the papacy, and had done nothing to hinder Stigand's authority until the papal legates arrived in England to depose the archbishop and reform the English Church.

Besides witnessing charters and consecrating Remigius, Stigand appears to have been a member of the royal council, and able to move freely about the country.

But after the arrival of the legates, William had done nothing to protect Stigand from deposition, and the archbishop will later accuse the king of acting with bad faith.

Stigand may even have been surprised that the legates wished him deposed.

It was probably the death of Ealdred in 1069 that had moved the pope to send the legates, as that left only one archbishop in England; and he is not considered legitimate and unable to consecrate bishops.

The historian George Garnett draws the parallel between the treatment of King Harold in Domesday Book, where he is essentially ignored as king, and Stigand's treatment after his deposition, where his time as archbishop is as much as possible treated as not occurring.