The Middle Ages was--broadly speaking--an age of deference to authority. This is why, in addition to the Bible, the four Doctors of the Church were held in such high esteem, and were relied upon so heavily in matters of dogmatic interpretation, particularly in the earlier medieval period, before the twelfth century renaissance. Initially, all medieval philosophers had to go on was Aristotle's Organon, translated by Boethius, as knowledge of Greek had been all but lost in the medieval west. Aristotle, while not being a Christian, was seen as being sufficiently authoritative on those logical subjects about which he wrote, due both to the age of his texts and the revolutionary mechanics of his thought, to be used by major intellectual figures of the pre-university Middle Ages, such as Abelard and, of course, Boethius himself. This, in turn, raised his profile. Everything changed with the rediscovery and translation of the larger corpus of Aristotle's work through the Arabic world. Imagine living in a world where authority is valued above all else, and then, suddenly, new texts from an ancient and known authority appeared. This was the intellectual world of the twelfth and thirteenth centuries. Thomas Aquinas happened to be flourishing just after their appearance on the western stage, and used the newly available works in the preparation of the Summa Theologiae, which not only made Thomas a theological rock star on the level of Peter Lombard, but necessitated the study of Aristotle by any subsequent scholar wishing to claim to be well-versed in philosophy.
While Aristotle could be forgiven for not being a Christian due to living prior to the Incarnation, the works of Aristotle did not go unopposed by Church authorities. The condemnations of 1210 - 1277 are the most important examples of this, being a series of condemnations issued by various authorities condemning and forbidding the study of Aristotle's physical treatises (among other writings) at the University of Paris. Similar condemnations were issued at Oxford sporadically from 1277 until virtually the end of the Middle Ages.
Grant, Edward. The Foundations of Modern Science in the Middle Ages: Their Religious, Institutional and Intellectual Context. Cambridge: Cambridge University Press, 1996.
Larsen, Andrew E. The School of Heretics: Academic Condemnation at the University of Oxford, 1277-1409. Leiden: Brill, 2011.
Thomas Aquinas. Laurence Shapcote, OP, trans. Summa Theologiae. Steubenville, Ohio: Emmaus Academic, 2018.