The honours course in Agriculture was introduced in 1958/59, and the June 1960 students were the first graduates with the honours classification. From 1948 to 1963 the University awarded degrees of the University of London under a scheme of special relationship. However, in 1963 the University received its own charter and became autonomous as the University of Ibadan and started to award its own degrees.

In 1962, the one-Department Faculty was split into four Departments of Agriculture, Agricultural Chemistry and Soils, Agricultural Biology and Agricultural Organization. By 1966-67 the four Departments were reorganized and respectively renamed Agronomy, Animal Science, Agricultural Biology and Agricultural Economics and Extension. In 1995, Agricultural Biology was renamed Crop Protection and Environmental Biology to reflect the multi-disciplinary nature of the Department.