Prejudice towards women is a recurrent theme throughout The Kingdom of Matthias. Matthews’s beliefs were rife with misogyny, and Johnson and Wilentz attribute his attitude to his Calvinist upbringing in communities that strictly enforced patriarchy. In Calvinist societies, then and now, families live by the gender oppression that characterizes their society as a whole. Fathers are responsible for leading prayers and commanding the household, and Church elders are uniformly male.

When Matthews moved to Manhattan, the Second Great Awakening threatened his role as patriarch. The Second Great Awakening, which took place from 1795 to 1835, was an evangelical movement that de-emphasized the role of the patriarch and highlighted instead the role of the mother as teacher and household leader. This progressive mindset intimidated Matthews, who responded by retreating to the familiar, conservative Old Testament beliefs he learned as a boy.

Other instances demonstrate the misogyny of Matthews and his followers. Pierson embraced Matthews’s misogynist doctrine after Pierson’s wife, Sarah, died. Matthews often whipped his wife Margaret and daughter Isabella, shows of abuse for which he was eventually arrested and convicted.

Matthews believed women to be tempters and seductresses who interfered with God's work. He believed that the Bible and his own visions proved that women were subordinate to men.