The Way of All Flesh charts Ernest’s transition from a believing, obedient child to a skeptical, independent adult as a natural result of Ernest’s experiences.

Throughout his youth, Ernest feels pain and sadness at his inability to measure up to his parents’ high, religiously-inflected expectations for him. Up to and even beyond the point of his ordination, Ernest never doubts the teachings of the church and his parents. The more he follows their counsel, the less happy he becomes but also the less aware he becomes of his own unhappiness, like a “very young foal trying to eat some most objectionable refuse, and unable to make up its mind whether it was good or no" (192). Only after a climactic experience lands him in prison does he begin to see a way forward.

Ernest proceeds to reevaluate everything he thought he knew through a new, rational lens. Finding inconsistencies in the Bible, he discards it as a source of ultimate truth, but he does not abandon faith entirely. Instead, the subject of his faith changes from the God of Christianity to “something as yet but darkly known which made right right and wrong wrong” (229). From that moment on, Ernest shows more interest in seeking knowledge than in enforcing adherence to any predefined system, such as the church.