Augustine’s search for truth would inevitably lead him to fall in with the pseudo-Christian sect known as the Manichees (followers of the self-declared prophet Mani). For close to ten years Augustine remained a Manichee and most of Book 3is spent on detailing his errors in falling in with them. Augustine’s first criticism of the Manichee doctrines he believed concerns their dependence on an elaborate mythology. The sun and moon are venerated as divine beings, and Manichees tended to picture divinity in terms of "physical images" or "bodily shapes." These "fantasies" and "dreams" will plague Augustine almost until his conversion, keeping him from recognizing God as a "spiritual substance" rather than some sort of enormous physical mass. Augustine offers a brief account of the proper view here, noting that God is not a body or even a soul (the life of the body). Rather, God is "the life of souls, the life of lives," more truthful and reliable than either bodies or the soul.

Augustine now turns to the three primary Manichee criticisms of Catholic belief (the refutation of these criticisms will be one of his central focuses toward the end of Confessions). The first, and most famous, Manichee challenge concerns the nature and source of evil. If God is supremely good, and if he is also all-powerful, eternal, and the cause of all existence, how can evil exist? Where can it come from except God? At the very least, why can't God eliminate it? Manichees insisted that God is not all-powerful and that he is in fact in constant struggle against his opposite, the dark, material world that is by nature evil. 

The second Manichee challenge concerns the nature of God as a being: "is God confined within a corporeal form? has he hair and nails?" This question is intimately tied to the question about evil, since it also challenges the idea of God as omnipotent and omnipresent. In the Manichee view, God is limited—he is not everywhere, and does not control everything. The rebuttal Augustine introduces to these first two challenges is Neoplatonic in nature, and its use for the defense of Catholic theology is one of the central achievements of his work. Simply put, God is Being itself, the most pure and supreme form of existence. Everything else is God's creation, and fits into a descending sale of Being—the further something is from God, the less true existence it has.

In general, Augustine faults the Manichees (and his own sinful lifestyle) for keeping him from understanding spiritual substance. Augustine then moves on to the third major Manichee challenge: the rejection of the book of Genesis and much of the Old Testament. The Manichees ridiculed the recurrence of polygamy and animal sacrifice in these parts of the bible, finding them in conflict with God’s laws as they are set out elsewhere in the bible. Augustine argues that, while God’s law is by definition eternal and unchanging, it reveals itself to humans by degrees and manifests itself differently according to the historical context. Dismissing, then, the Manichee criticisms of Old Testament behavior, Augustine sketches out a brief classification of kinds of sin. Augustine proceeds to note a few cases where it may be unclear to what extent an act is sinful. Some sinful acts, such as animal sacrifice, may be justifiable if they are prophetic acts (as was the case with the sacrifices in the Old Testament). In the end, Augustine had nothing but pity and a lingering disgust with Manicheans.