Influenced by European higher criticism of the Bible and advances in science, Toy began intellectual pursuits that would ultimately cost him his tenure at Southern.

Shaped by the historical-critical method of studying scripture that had been popularized in Europe by Julius Wellhausen, Toy came to believe that the writers of the New Testament—using a rabbinical hermeneutic of their day—misunderstood the original meaning of several Old Testament passages (e.g., Psalm 16:10, Isaiah 53) when they placed a Christological emphasis on them.

[3] The founding president of Southern, Dr. James P. Boyce, asked Toy to refrain from teaching contrary to the school's Abstract of Principles on the doctrine of biblical inspiration.

[4] In addition to his controversy at Southern Seminary, Toy is also famous for teaching and once being engaged to Lottie Moon, for whom the SBC annual Christmas offering for international missions is named.

In her 1881 correspondence with Southern Baptist Foreign Mission Board secretary H. A. Tupper, Moon expressed her plans to marry Toy, who was now a professor at Harvard.