In November 1654 Oliver Cromwell described him to his son Henry Cromwell as a dangerous man who should be secured in a safe place.
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On 14 August 1657 he was ordained at Winwick, Lancashire, by the fourth Lancashire presbyterian classis; this was on a call from the parish of Dunboyne, County Meath, where he had officiated from 1655, with a stipend under the civil establishment of Henry Cromwell.
He was the brother-in-law of Sir William Clarke, Secretary to the Army, and kept in touch with him as a news source; he also regularly corresponded with Henry Cromwell, Lord Lieutenant of Ireland.
Thomas Stanley (died 1674) of Grangegorman, Dublin, was knighted by Henry Cromwell Lord Deputy of Ireland on 24 January 1659 at Dublin Castle.
His father has been described as a remarkable man who through a long career was able to work with Viceroys as different as the Earl of Strafford, Henry Cromwell, and James Butler, 1st Duke of Ormonde.
Anne Cromwell was born in 1618, the youngest child of Henry Cromwell († 1630) of Upwood, now in Cambridgeshire.