From 1268 and until 1272 Thomas was again in Paris where he took up the most important teaching position, that of Master of theology. From this period there are the second inaugural lectures of the courses, the Lectura super Matthaeum and the most profound Lectura super Johannem. Thomas was also employed in finishing the Summa theologiae and worked in polemics, arguing again against the secular Masters opposed to the mendicants. He could also be found in engaging and confronting the anti-Aristotelian conservatives among the Augustinian theologians. Again he set himself against the theory of monopsychism originating with Averroes and against the assertion held by the radical Averroists (for example Siger of Brabant) about the independence of philosophy from revelation. Afterwards, owing to a debate at the university, he wrote De aeternitate mundi in which he sets forth the principle that it is only by faith that we believe the world has a beginning, while he reasons that the contrary cannot be proved. In De unitate intellectus contra Averroistas, he defends the christian faith but also Aristotelian philosophy in the controversy about the possible intellect as one, single separate substance for all men.

In this period Thomas would carry on different theological discussions tied to the problem of evil which are collected in the Quaestiones disputatae, De malo. From the midst of this intense activity there also came seven Quodlibetales, and other short writings arguing on different questions: De mixtio elementorum, De motu cordis, De occultis operationiibus naturae, De iudiciis astrorum, De sortibus, De secreto, De regimine Judaeorum ad Ducissam Brabantiae, and the incomplete De substantiis separatis, a theological tract with metaphysical value, about the angels that are the foundation of the writings of Pseudo-Dionysius. In the Expositio super librum de causis Thomas comments on the neoplatonic philosophy that he formerly believed to be by an Arabic author influenced by the thought of Proclus.

In Paris he also a wrote commentaries on Aristotle. There were the incomplete Expositio libri Peri hermenias and the Expositio libri Posteriorum, works requested by the Parisian Masters before Thomas's death. The Sententia libri Ethicorum was a simplified but doctrinal commentary on the ethics of Aristotle in which Thomas sensibly transforms Aristotle's pagan morality. The Tabula libri Ethicorum, an incomplete index file of the principle terms in the Nicomachean Ethics of Aristotle and in a commentary of Albert of Cologne, was useful to Thomas and his secretaries in drafting the Secunda pars of the Summa. The commentaries on the Physica, the Sententia super Physicam, and the Metaphysica, the Sententia super Metaphysicam, of Aristotle were finished at Naples. The Sententia libri Politicorum remains incomplete, as do the Sententia de coelo et mundo and the Sententia super Meteora. The Sententia super libros De generatione et corruptione, also incomplete, was composed at Naples towards the end of this life.