- "An Elementary German Grammar" (1870): This book was widely used as a textbook for teaching German in American schools and colleges. It is designed for beginners and provides an introduction to the basics of German grammar.
- "A German Reader" (1880): This is a collection of German literary pieces selected for their language value and cultural significance. It was intended for students who have some familiarity with German and want to improve their reading skills.
- "German Literature" (1890): This is a comprehensive history of German literature from its origins to the late 19th century. It covers major literary figures, movements, and works, providing an overview of German literary development.
- "The German Question: A Study in Nationalism" (1892): In this book, Joynes analyzes the political, social, and historical factors that shaped the development of German nationalism. He examines how these factors influenced the course of German history and its impact on European affairs.
- "Life of Dr. Frederic Henry Hedge" (1899): This is a biography of Frederic Henry Hedge, a prominent American Unitarian minister, theologian, and scholar. Joynes provides a detailed account of Hedge's life, his contributions to religious thought, and his influence on American intellectual life.
Joynes also edited and contributed to various educational journals and publications. He was a proponent of modern language education and was actively involved in promoting the teaching of foreign languages in American schools.