She was impatient with traditional Christianity

Susan B. Anthony was a Quaker at first and then grew more involved with the Unitarians despite having a maternal grandfather who had been a Universalist. Like many others of her era, she dabbled with Spiritualism, the notion that spirits were a component of the natural world and could thus be interacted with. Although she advocated the publication of "The Woman's Bible" and condemned religious organizations and doctrines that represented women as inferior or subordinate, she largely kept her religious beliefs a secret.

Her criticism of religious organizations and how religion is conducted is typically the basis for assertions that she was an atheist. Susan B. Anthony fought for Ernestine Rose's ability to lead the National Women's Rights Convention in 1854, even though many people incorrectly referred to Rose, a Jew who was married to a Christian, as an atheist. Regarding that debate, Anthony stated, "Every religion, or none at all, should have an equal right on the platform." “I distrust those people who know so well what God wants them to do because I notice it always coincides with their desires,” she added in another letter. At another time, she wrote, “I shall earnestly and persistently continue to urge all women to the practical recognition of the old Revolutionary maxim. Resistance to tyranny is obedience to God.”

It's unclear if she was an atheist or simply had a different conception of God than some of her evangelical opponents.