Xenophanes' surviving writings display a skepticism that became more commonly expressed during the fourth century. He cleverly satirized the polytheistic beliefs of earlier Greek poets and of his own contemporaries: "Homer and Hesiod" one fragment states, "have attributed to the gods all sorts of things that are matters of reproach and censure among men: theft, adultery, and mutual deception." Sextus Empiricus reported that such observations were appreciated by Christian apologists. Xenophanes is quoted, memorably, in Clement of Alexandria, arguing against the conception of gods as fundamentally anthropomorphic:

But if cattle and horses and lions had hands
or could paint with their hands and create works such as men do,
horses like horses and cattle like cattle
also would depict the gods' shapes and make their bodies
of such a sort as the form they themselves have.
...
Ethiopians say that their gods are snub – nosed [σιμούς] and black
Thracians that they are pale and red - haired.

Other passages quoted by Clement of Alexandria that argue against the traditional Greek conception of gods include:

1. "One god, greatest among gods and humans,
   like mortals neither in form nor in thought."
2. Two "But mortals think that the gods are born
   and have the mortals' own clothes and voice and form"

Regarding Xenophanes' theology five key concepts about God can be formed. God is: beyond human morality, does no resemble human form, cannot die or be born (God is divine thus eternal), no divine hierarchy exists, and God does not intervene in human affairs. While Xenophanes is rejecting Homeric theology, he is not questioning the presence of a divine entity, rather his philosophy is a critique on Ancient Greek writers and their conception of divinity. There is also the concept of God being whole with the universe, essentially controlling it, while at the same time being physically unconnected. It would seem, however, that this notion of God being intertwined with the universe contradicts Xenophanes' physical philosophy.

Xenophanes espoused a belief that "God is one, supreme among gods and men, and not like mortals in body or in mind." He maintained there was one greatest God. God is one eternal being, spherical in form, comprehending all things within himself, is intelligent, and moves all things, but bears no resemblance to human nature either in body or mind. He is considered by some to be a precursor to Parmenides and Spinoza. Because of his development of the concept of a "one god greatest among gods and men" that is abstract, universal, unchanging, immobile and always present, Xenophanes is often seen as one of the first monotheists, in the Western philosophy of religion, though this vision is disputed.

Xenophanes wrote about two extremes predominating the world: wet and dry (water and earth). These two extreme states would alternate between one another and with the alteration human life would become extinct then regenerate (or vise versa depending on the dominant form). The idea of alternating states and human life perishing and coming back suggests he believed in the principle of causation; another distinguishing step that Xenophanes takes from Ancient philosophical traditions to ones based more on scientific observation. The argument can be considered a rebuke to Anaixmenes' air theory. A detailed account of the wet and dry form theory is found in Hippolytus' Refutation.

Xenophanes concluded from his examination of fossils that water once must have covered all of the Earth's surface. The use of evidence is an important step in advancing from simply stating an idea to one being back up by evidence and observation.

Xenophanes is credited with being one of the first philosophers to distinguish between true belief and knowledge, which he further developed into the prospect that you can know something but not really know it. If the statement seems unclear, that's because it is. Due to the lack of whole works by Xenophanes a lot of meaning is lost and a whole lot of guessing is at hand, so that the implication of knowing being something deeper ("a clearer truth") may have special implications or it just may mean that you cannot know something just by looking at it. It is known that the most and widest variety of evidence was considered by Xenophanes to be the surest way to prove a theory.

His epistemology, which is still influential today, held that there actually exists a truth of reality, but that humans as mortals are unable to know it. Karl Popper read Xenophanes as saying that it is possible to act only on the basis of working hypotheses — we may act as if we knew the truth, as long as we know that this is extremely unlikely. Xenophanes' views then might serve as a basis of Critical rationalism.

In today's philosophical and classics discourse, Xenophanes is seen as one of the most important presocratic philosophers. It had also been common since antiquity to see him as the teacher of Zeno of Elea, the colleague of Parmenides, and generally associated with the Eleatic school, but common opinion today is likewise that this is false (e.g., Lesher).

There is one fragment dealing with the management of a feast, another which denounces the exaggerated importance attached to athletic victories, and several which deny the humanized gods of Homer. Arguments such as these made Xenophanes infamous for his attacks on "conventional military and athletic virtues of the time" and well known to side with the intellectual instead.