Adams published several articles and reviews before his first history, The Emancipation of Massachusetts (1887). In it, Adams attacked the hagiographic depictions of the Protestant forefathers of New England. He argued that previous depictions of early New England founders were untrue and that, instead of fostering democratic virtues, the founders engendered a climate of religious intolerance. The book was perceived as controversial in its time, and much was made of the unbalanced nature of Adams's presentation. Adams's defended his work to Henry Cabot Lodge: "It is really not a history of Mass. but a metaphysical and philosophical inquiry as to the actions of the human mind in the progress of civilization; illustrated by the history of a small community isolated and allowed to work itself free. This is not an attempt to break down the Puritans or to abuse the clergy, but to follow out the action of the human mind as we do of the human body. I believe they and we are subject to the same laws." While declaring his premise sound for the original, Adams added a 168-page preface to his 1919 revision, which many critics believe refutes the theories of his original manuscript.

In his next major work, The Law of Civilization and Decay: An Essay on History (1895), Adams examined the control of economic power and its effect on history, politics, culture, and religion. Adams posited that the cyclical nature of centralization and stagnation was governed by physical laws. Civilization, wrote Adams, followed a set pattern of stages: energy-gathering, which incorporated imagination, war and conquest; centralization and the accumulation of wealth; and usurpation of energy by capitalists. Once economic power is centralized in a civilization, greed becomes predominant, leading to stagnation in all elements of society. Adams supported his thesis using ancient Rome, Medieval Europe, and Imperial Britain as examples. When economic power became centralized in any of these areas, stagnation set in and this power moved elsewhere. While finding Adams's methodology unsystematic, critics received The Law of Civilization and Decay positively. The perception that Adams was disenfranchised from American capitalism and was predicting the eventual demise of the U.S. economy was reinforced by his subsequent efforts. America's Economic Superiority (1900), The New Empire (1902), and The Theory of Social Revolutions (1913) continued his theories into economic history. He also wrote the preface to brother Henry Adams's The Degradation of the Democratic Dogma (1920).