He returned to Hyderabad in 1948 and joined Osmania University as an associate professor.
Later he was transferred to Sindh University, Jamshoro as chairman of the Zoology Department.
[1] In 1978, Mohiuddin joined Quaid-e-Azam University as Vice Chancellor and later became Vice Chancellor of Allama Iqbal Open University in Islamabad, Pakistan.
He was awarded a fellowship from Pakistan Academy of Sciences and Royal Society of Tropical Medicine.
In recognition of his services to the field of zoology, Zoological Society of Pakistan created the Ahmed Mohiuddin Memorial Gold Medal for talented students awarded nationally in Pakistan.