After completing her PhD in 1951, she returned to Australia and joined the Department of Microbiology at the University of Melbourne. She worked as a demonstrator and then as a lecturer, setting up the Applied Microbiology course at the University. In 1954, she was awarded a Fulbright Travel Grant and she went to Hopkins Marine Station at Stanford University and worked with C B Van Neil, and then to the Institute of Applied Microbiology at the University of Tokyo.

Prof Millis was one of five Australian scientists recognized on the ‘Australian Legends' series of stamps in 2002. She also has to her credit a string of scientific and civic accolades, including election to the Australian Academy of Science, an MBE and a Companion of the Order of Australia. On her retirement, the International Journal of Systematic and Evolutionary Microbiology reported a newly discovered bacterium named Millisa brevis in recognition of her contribution to water microbiology.