He remained in California until 1942, when he became an assistant curator of Lepidoptera at the American Museum of Natural History in New York City.

From 1943 to 1946, Michener also served as a first lieutenant and captain in the United States Army Sanitary Corps, where he researched insect-borne diseases, and described the life cycle of the common chigger.

He was awarded the Watkins Distinguished Professor of Entomology in 1958, won a Fulbright Scholarship to Australia in 1958, was elected to the National Academy of Sciences in 1965, and became director of the Snow Entomological Museum (now part of the University of Kansas Natural History Museum, itself now a division within the University of Kansas Biodiversity Institute) in 1974.

Hawkins Award for the Outstanding Professional Reference or Scholarly Work of 2000 to Michener's opus, The Bees of the World.

Michener's long career also included the training of more than 80 master's and doctoral students, among them Jim Baker, Edward M. Barrows, Suzanne W. T. Batra, Michael D. Breed, Denis Brothers, Sydney Cameron, Jim Cane, Paul R. Ehrlich, George Eickwort, Les Greenberg, William Gutierrez, Alexander Hawkins, Dwight Kamm, Robert Minckley, William Ramirez, Radclyffe Roberts, Brian H. Smith, Thomas Snyder, William Wcislo, John Wenzel, Alvaro Wille, and Douglas Yanega.