Already known for securing government contracts for himself, as well as his brothers and friends, he offered land to establish the Choctaw Academy, a school devoted to the European-American education of Indians from the Southeast tribes. Johnson had tried to establish an Indian school at Great Crossings in 1818, partnering with the Kentucky Baptist Society, but the school folded in 1821 after it failed to gain the support of the federal government or private donors. The new academy would come into being a few years later. The academy, sitting on his farm in Scott County in 1825, was overseen by Johnson; and not only was part of treaty negotiations with the Choctaw Nation but appealed to his colleagues as a form "peaceful conquest" or "expansion with honor" as Henry Knox put it. Although he never ran afoul of the conflict of interest standards of his day, some of his colleagues considered his actions ethically questionable. Johnson was paid well for the school by the federal government, which gave him a portion of the annuities for the Choctaw. It was promoted by the Baptist Missionary Society as well. Some European-American students also attended the Academy, including his nephew Robert Ward Johnson from Arkansas.