J. A. Atanda is a scholar of the Yoruba to the core. Throughout his lifetime, he predominantly wrote on and taught various aspects of Yoruba history and culture. His affection for the history of his people blossomed into various major essays on themes ranging from indirect rule and intergroup relations among the Yoruba to Yoruba intellectual history. In addition, he also wrote about such debated issues as the origin of the Yoruba people, theories of the fall of the Old Oyo Empire, and the place of secret societies in Yoruba history and culture.

Although Bolanle Awe and Atanda both work on Yoruba history, each has primary and concentrated interests in a different part of Yorubaland. While Awe's PhD thesis and early essays deal predominantly with nineteenth-century Ibadan history, Atanda addresses how colonial rule changed intergroup relations between Oyo and its neighbors. The two historians sometimes examine Yoruba-wide themes. Awe concentrates more on nineteenth-century Yoruba history, while Atanda's scholarship stretches from the eighteenth to the twentieth century. Other well-published historians of the Yoruba are S. A. Akintoye, I. A. Akinjogbin, J. F. Ade Ajayi, G. O. Oguntomisin, and Toyin Falola. Atanda's scholarship also extends to mission studies. He edited two books, one on Baptist churches in Nigeria and the other the account of Yorubaland in the 1850s by W. H. Clarke, a Baptist missionary.

Colonialism and Indirect Rule

Atanda's most widely read work, The New Oyo Empire, is a revised version of his PhD thesis for the University of Ibadan in 1967. The work looks at how the British, during the colonial period (1893–1960), succeeded in creating a huge political arrangement meant to resemble, in terms of size and influence, the Old Oyo Empire, which was destroyed around the second decade of the nineteenth century, and its effects on relations between the Oyo and its neighbors.