In the ecclesiastical field he threw the weight of his learning into the drive against Puritan and Brownist opinions in Church and university ( 1587-90 ), and took part in the condemnation of his distant kinsman John Penry in 1593 ; he was also consulted by Grindal on the reform of the Church courts in the province of Canterbury , of which he became joint administrator ( 1577 ) and then sole vicar-general ( 1582 ) during Grindal 's suspension, retaining the office under Whitgift ( 1583 ), and conferring by means of it many favours on his countrymen. In that of international law he sat on the commission ( 1571 ) which pronounced the bishop of Ross — ambassador from the Queen of Scots with whom he is said to have sympathized ( Aubrey , Lives , 15; Hist. MSS. Com. , Cent. , i, 542) — amenable to English courts in respect of his intrigues against Elizabeth , and many of his decisions in maritime law (especially on questions arising out of the naval war with Spain ) had important international bearings; he was also concerned in the suppression of Welsh piracy and was privately retained as counsel (much to their advantage) by the Merchant Adventurers .

Questions of jurisdiction in Wales , Ireland , and the Channel Islands were among those he resolved in the sphere of constitutional law, and he was brought into even more direct contact with politics when his kinsman and benefactor Henry Herbert , 2nd earl of Pembroke , captain-general of queen Mary 's expeditionary force to France , took Aubrey with him as Judge Advocate ( 1557 ), as a member of archbishop Parker 's commission which declared the illegality of Lady Catherine Grey 's marriage with Hertford ( 1552 ) — a case involving the succession to the throne — and in the petitions and legal questions referred to him as Master of Requests ( 1590-5 ) by Burghley and the Privy Council .

In many of his major decisions he was associated with other Welsh civil lawyers such as T. Yale (see Yale family ), David Lewis , and Henry Johnes . In Wales itself he was M.P. for Carmarthen ( 1554 ) and Brecon ( 1558 ), J.P. and sheriff ( 1545 ) for Brecknock , and a member of the Council of Wales ( 1586 ). He acquired extensive estates in Brecknock and other parts of South Wales both by purchase and by royal grant, visiting them periodically ‘to make merye with his frendes’ ( Stradling Correspondence , 26, 312). He is said to have died worth £2,500 a year, much of which was lost to his legatees through a fraudulent executor . He was a friend, neighbour, and correspondent of his kinsman John Dee . He was buried in old S. Paul's , where a monument in bas-relief showed him surrounded by the kneeling figures of his three sons (who erected it) and six daughters, describing him as ‘a man of exquisite erudition, singular prudence, and great courtesy’ (reproduced Dugdale , St. Paul's , 1716 , 98-9).