In an extremely grave crisis, teetering towards civil war during the years from 1386 through 1388, the bishop found himself, at least in formal terms, right at the front of the dangerous attempts by five leading temporal lords to purge the king's advisors and control future policy.

On 3 April 1388, Arundel was elevated to the position of Archbishop of York[3] at a time when Richard II was, in effect, suspended from rule.

Despite his political preoccupations, which certainly led to him being largely absent from York, he has been credited with sponsoring a lively revival of personal religious piety in the northern province.

Arundel played a prominent part in the usurpation and may have been the most hawkishly determined of all that the king should be removed entirely: whether he actually lied under oath to Richard II to lure him out of Conwy Castle remains open to debate.

In 1405–06 he had to deal with the crisis with the papacy provoked by the king's decision to execute the archbishop of York, Richard Scrope, who had participated in the Percy rebellion.

Arundel was a vehement opponent of the Lollards, the followers of John Wycliffe, who in his 1379 treatise De Eucharistia had opposed the dogma of Transubstantiation and whose theology of dominium denied the legitimacy of any secular and clerical authorities concluded to be in mortal sin.

King Henry IV passed the De heretico comburendo statute in 1401, which recited in its preamble that it was directed against a certain new sect "who thought damnably of the sacraments and usurped the office of preaching.

"[8] It empowered the bishops to arrest, imprison, and examine offenders and to hand over to the secular authorities such as had relapsed or refused to abjure.

[8] In 1407, Arundel presided at a synod at Oxford, which passed a number of constitutions to regulate preaching, the translation and use of the Scriptures, and the theological education at schools and the university.

[9] In 2005/2006, BBC History Magazine chose Thomas Arundel as the 15th century's entry for their Ten Worst Britons poll,[10][11] in which he tied in ninth place with Hugh le Despenser.