Quarles married twice: first to Vera Bullock Quarles, who died in 1951;  and then to Ruth Brett, 1952. Ruth Brett Quarles outlived her husband. They had two daughters.

There were few sympathizers at Wisconsin for Quarles's desires to write black history. "There was a feeling that a black person studying black history would turn it into propaganda," he later recalled. Nevertheless, Quarles stuck to his plan, and eventually found a professor who consented to guide his thesis research.

Much of Quarles writing style was learned from Professor William Hesseltine of the University of Wisconsin with whom he worked while completing his doctorate. It was a smooth  narrative mask of objectivity. Yet as Wilson Jeremiah Moses, points out in History Teacher (1998), "his persistent efforts to demonstrate the centrality of blacks in building. American civilization, and his criticism of those who did not share his belief in the mission of the United States in the world, show he was a conceptual historian with a clear agenda."

Quarles' second book, The Negro in the Civil War, appeared in 1953, the year he moved to Morgan State College in Baltimore, Maryland, to chair the department of history. In this work he set out to show the deep flaw in the traditional picture of slaves as passive pawns in the fight against slavery. On the contrary, he asserted, 3.5 million African Americans had been major participants in the struggle for democracy, 180,000 of them working as soldiers, and the rest as orderlies, spies, and laborers.

“Milliken’s Bend,” said Quarles, “was . . . [near Vicksburg, Mississippi] one of the hardest fought encounters in the annals of American military history." Its lesson was not lost on the Union high brass: “The bravery of the Blacks at Milliken’s Bend,” observed Assistant Secretary of War Charles A. Dana, “completely revolutionized the sentiment of the army with regard to the employment of Negro troops.”

In his next major work, The Negro in the American Revolution, Quarles enlarged upon the theme of black Americans as major players in their own search for freedom. He was the the first to cast any light at all on the topic of the African American contribution to the revolution itself. "Unlettered, they put very little down on paper. If they are to be understood, it must be primarily by what they did. Hence, especially in the pages of this work dealing with the Negro acting of his own volition, my approach has been to state the facts about his activities, indicate the documentary sources, and as far as possible avoid conjecture as to his unrecorded thought," he continued.

His next book Lincoln and the Negro, Quarles attempted to show Lincoln the president as a true friend of the enslaved. For Lincoln opposed slavery  opposed slaver because of the philosophy expressed in the Declaration of Independence. Yet Lincoln also believed that blacks were mentally inferior to whites, that  intermarriage was unworthy, and was non-supportive of voting rights for black Americans. Quarles still concluded: "In the story they would relate to their children, Negroes would lay stress on the enduring Lincoln, in whom death was swallowed up in victory."

All his previous works were a prelude to his 1969 publication, Black Abolitionists. In this work Quarles challenged the accepted view that abolitionists had been primarily white reformers. There were blacks carrying the anti-slavery banners as early as the1830s. These black abolitionists spiritedly opposed efforts to colonize all black Americans in Africa, and resented the paternalization of missionary whites determined to uplift them willy-nilly. Quarles also reminded the historical community that new Negro newspapers had emphasized the non-white viewpoint, insisting on voting, civil, and human rights for an audience of both black and white readers.

For the journal Daedalus, Quarles wrote one of his last thought-provoking essays. He concluded, "The role of blacks in America—what they have done and what has been done to them—illuminates the past and informs the present. Unless we fully comprehend the role of racism in this society, we can never truly know America."