In the treatise, Spinoza put forth his most systematic critique of Judaism, and all organized religion in general. Spinoza argued that theology and philosophy must be kept separate, particularly in the reading of scripture. Whereas the goal of theology is obedience, philosophy aims at understanding rational truth. Scripture does not teach philosophy and thus cannot be made to conform with it, otherwise the meaning of scripture will be distorted. Conversely, if reason is made subservient to scripture, then, Spinoza argues, "the prejudices of a common people of long ago... will gain a hold on his understanding and darken it."

Spinoza argued that purportedly supernatural occurrences, namely prophecy and miracles, have in fact natural explanations. He argued that God acts solely by the laws of his own nature and rejected the view that God acts for a particular purpose or telos. For Spinoza, those who believe that God acts for some end are delusional and projecting their hopes and fears onto the workings of nature.