Al-Ghazâlî describes the Incoherence of the Philosophers as a “refutation” (radd) of the philosophical movement (Ghazâlî 1959a, 18 = 2000b, 61), and this has contributed to the erroneous assumption that he opposed Aristotelianism and rejected its teachings. His response to falsafa was far more complex and allowed him to adopt many of its teachings. The falâsifa are convinced, al-Ghazâlî complains at the beginning of the Incoherence, that their way of knowing by “demonstrative proof” (burhân) is superior to theological knowledge drawn from revelation and its rational interpretation. This conviction led “a group” among the Muslim falâsifa to disregard Islam and to neglect its ritual duties and its religious law (sharî’a). In his Incoherence al-Ghazâlî discusses twenty key teachings of the falâsifa and rejects the claim that these teachings are demonstratively proven. In a detailed and intricate philosophical discussion al-Ghazâlî aims to show that none of the arguments in favor of these twenty teachings fulfills the high epistemological standard of demonstration (burhân) that the falâsifa have set for themselves. Rather, the arguments supporting these twenty convictions rely upon unproven premises that are accepted only among the falâsifa, but are not established by reason. By showing that these positions are supported by mere dialectical arguments al-Ghazâlî aims to demolish what he regarded was an epistemological hubris on the side of the falâsifa. In the Incoherence he wishes to show that the falâsifa practice taqlîd, meaning they merely repeat these teachings from the founders of their movement without critically examining them (Griffel 2005).

The initial argument of the Incoherence focuses on apodeixis and the demonstrative character of the arguments refuted therein. While the book also touches on the truth of these teachings, it “refutes” numerous positions whose truths al-Ghazâlî acknowledges or which he subscribed to in his later works. In these cases al-Ghazâlî wishes to show that while these particular philosophical teachings are sound and true, they are not demonstrated. The ultimate source of the falâsifa's knowledge about God's nature, the human soul, or about the heavenly spheres, for instance, are the revelations given to early prophets such as Abraham and Moses. Their information made it into the books of the ancient philosophers who falsely claimed that they gained these insights by reason alone.

Among the twenty discussions of the Incoherence, sixteen are concerned with positions held in the falâsifa's metaphysics (ilâhiyyât) and four with positions that appear in their natural sciences (tabî’iyyât). The 17th discussion on causality will be analyzed below. The longest and most substantial discussion is the first, which deals with Avicenna's and al-Fârâbî's arguments in favor of the world's pre-eternity (Hourani 1958, Marmura 1959). Al-Ghazâlî denies that this position can be demonstratively proven and draws from arguments that were earlier developed by anti-Aristotelian critics such as the Christian John Philoponus (Yahyâ l-Nahwî, c.490–c.570) of Alexandria. Philoponus' arguments, most importantly those that deny the possibility of an infinite number of events in the past, had entered the Arabic discourse on the world's creation earlier during the 9th century (Davidson 1987, 55–56, 86–116, 366–75).

At the end of the Incoherence al-Ghazâlî asks whether the twenty positions discussed in the book are in conflict with the religious law (sharî’a). Most of them are wrong, he says, yet pose no serious problems in terms of religion, where they should be considered “innovations” (singl. bid'a). A small group of positions is considered wrong as well as religiously problematic. These are three teachings from Avicenna's philosophy, namely (1) that the word has no beginning in the past and is not created in time, (2) that God's knowledge includes only classes of beings (universals) and does not extend to individual beings and their circumstances (particulars), and (3) that after death the souls of humans will never again return into bodies. In these three cases the teachings of Islam, which are based on revelation, suggest the opposite, al-Ghazâlî says, and thus overrule the unfounded claims of the falâsifa. What's more, these three teachings may mislead the public to disregarding the religious law (sharî’a) and are, therefore, dangerous for society (Griffel 2000, 301–3). In his function as a Muslim jurisprudent al-Ghazâlî adds a brief fatwâ at the end of his Incoherence and declares that everybody who teaches these three positions publicly is an unbeliever (kâfir) and an apostate from Islam, who can be killed (al-Ghazâlî 2000a, 226).

Al-Ghazâlî's efforts in dealing with the philosophical movement amount to defining the boundaries of religious tolerance in Islam. Soon after the Incoherence, he wrote a similar book about the movement of the Ismâ’îlite Shiites, known as the “Bâtinites” (“those who arbitrarily follow an inner meaning in the Qur’an”). Initially the Ismâ’îlite Shiites were supporters of the Fâtimid counter-caliphate in Cairo and opposed the political and religious authority of the Sunni caliph in Baghdad and the Seljuq Sultans that he installed. During al-Ghazâlî's lifetime, however, there occurred a schism within the clandestine Ismâ’îlite movement. The “new propaganda” of the Ismâ’îlites in Iraq and Iran was now independent from the center in Cairo and developed its own strategies. A key element of their—not entirely unsuccessful—efforts to persuade people to their camp was their criticism of sense perception and of rational arguments (al-Ghazâlî 1954, 34; 1964b, 76, 80). Al-Ghazâlî was closely familiar with the Ismâ’îlites' propaganda efforts but he had little reliable information on their teachings on cosmology and metaphysics. These were deeply influenced by cosmological notions in late antique Gnostic and Neoplatonic literature (Walker 1993, de Smet 1995). Al-Ghazâlî also did not know about the schism within the movement. In his book on the Scandals of the Esoterics (Fadâ’ih al-Bâtiniyya) he looks closely at those teachings that he knew and discusses which of them are merely erroneous and which are unbelief. He assumes—wrongly—that the Ismâ’îlite propagandists teach the existence of two gods. This dualism and the Ismâ’îlites' denial of bodily resurrection in the afterlife leads to their condemnation by al-Ghazâlî as unbelievers and apostates (al-Ghazâlî 1964b, 151–55 = 2000b, 228–29).