Aylmer became a principal agent of Thomas Cromwell in Ireland and worked closely with John Alan, Master of the Rolls in Ireland, in bringing about the defeat of Silken Thomas. He assisted various English lord deputies in Ireland in expeditions against the O'Connors and the Kavanaghs and was employed in military campaigns against the Geraldines and the O'Neills. He was knighted in the field after the battle of Bellahoe in 1539, and given a grant of the lands of Dollardstown, near Athy, County Kildare
Suppression of the Monasteries
Aylmer and John Alan travelled to England in 1536 to receive the bill for suppression of the Irish monasteries, bringing the legislation to the Reformation Parliament of 1536–7. The resulting Act involved in the first instance the suppression of the monastery of St Wolstan's, near Celbridge, Co Kildare, and assured Aylmer and his fellow chief justice and brother-in-law Thomas Luttrell an annual rent of £4 during the life of Sir Richard Weston, the last prior: in 1538 St. Wolstan's itself was granted to John Alan and his heirs. Aylmer joined with Alan and others in the comprehensive commission to dissolve other Irish monastic houses, gaining profitable estates in County Meath. He conducted an inquisition at Limerick of ecclesiastical shrines in 1541, and he obtained the Franciscan friary at Drogheda by patent of 16 February 1543 for the price of £54 17s. 3d. Despite his loyalty to Henry it is not clear whether he was committed to the Protestant faith: it was not unusual then for members of the Anglo-Irish gentry class to which he belonged to conform to the reformed faith outwardly while remaining secretly loyal to the Roman Catholic church. Later generations of the Aylmer family, including the Barons Aylmer, were mainly Catholic.
Opposition to Lord Grey
Aylmer opposed the policy of the new Lord Deputy of Ireland, Leonard Grey after Silken Thomas's rebellion was quashed in 1536, and campaigned with John Alen to undermine Grey's administration. Aylmer attended Sir Anthony St Leger to London in 1538, joining the commission of inquiry to bring charges against Grey.
Three Monarchs
Aylmer was knighted in 1539 and survived the downfall of both Grey and Cromwell in 1540 to serve under Henry's successors as King and Queen of England, Edward VI and Elizabeth I, being reappointed Chief Justice on 24 March 1547 and on 16 November 1553. In 1541 he was among the Irish lawyers who petitioned for a lease of Blackfriars monastery in Dublin to establish the predecessor of the King's Inns there.
Later life
Aylmer was named Lord Justice of Ireland along with Sir Thomas Cusack on 6 December 1552 and eventually dropped from the Privy Council of Ireland in 1556 when the new viceroy, Thomas Radclyffe, 3rd Earl of Sussex, replaced the appointees of his predecessor St Leger. Aylmer now came infrequently to the Irish council and Elizabeth wrote in 1559 that she wished to promote another Old English lawyer, John Plunket, to the office of Chief Justice in his place.
Aylmer family
His kinsman and namesake Sir Gerald Aylmer of County Kildare, perhaps a son, was a leader of opposition to the cess among the Pale grandees of the 1580s. His eldest son Bartholomew predeceased him, but left three surviving sons of whom James succeeded to his grandfather's estates, while Christopher founded a junior branch of the family with its seat at Balrath, County Meath, which in time acquired the title Baron Aylmer. Aylmer's descendants resided at Lyons, Ardclough Co Kildare until 1796 when the property passed to the Lord Cloncurry, father of Valentine Lawless. It later became the homestead of aviation pioneer Tony Ryan.
