In his work within marine biology, cytology and parthenogenesis, he advocated the study of whole cells under normal conditions, rather than simply breaking them apart in a laboratory setting.

[4] Just was a candidate to deliver a commencement speech, but was not chosen because the faculty "decided it would be a faux pas to allow the only black in the graduating class to address the crowd of parents, alumni, and benefactors.

However, Just worked to mediate the controversy and, despite the initial doubts, Omega Psi Phi, Alpha Chapter, was chartered on Howard's campus on December 15, 1911.

Not long after beginning his appointment at Howard, Just was introduced to Frank R. Lillie, the head of the Department of Zoology at the University of Chicago.

He investigated the fertilization reaction and the breeding habits of species such as Platynereis megalops, Nereis limbata, and Arbacia punctulata.

While at the MBL, Just learned to handle marine invertebrate eggs and embryos with skill and understanding, and soon his expertise was in great demand by both junior and senior researchers alike.

That same year, Just, who was gaining a national reputation as an outstanding young scientist, was the first recipient of the NAACP's Spingarn Medal, which he received on February 12, 1915.

By the time he received his doctorate from Chicago, he had already published several research articles, both as a single author and a co-author with Lillie.

He was condemned by racism to remain attached to Howard, an institution that could not give full opportunity to ambitions such as the ones Just had due to budgetary constraints of the era.

Then, in 1930, he became the first American to be invited to the Kaiser Wilhelm Institute in Berlin-Dahlem, Germany, where several Nobel Prize winners carried out research.

He moved his European-based studies to Paris and to the marine laboratory at the French fishing village of Roscoff, located on the English Channel.

Just authored two books, Basic Methods for Experiments on Eggs of Marine Animals (1939) and The Biology of the Cell Surface (1939), and he also published at least seventy papers in the areas of cytology, fertilization and early embryonic development.

[13] He believed that the conditions used for experiments in the laboratory should closely match those in nature; in this sense, he can be considered to have been an early ecological developmental biologist.

[14] His work on experimental parthenogenesis informed Johannes Holtfreter's concept of "autoinduction"[15] which, in turn, has broadly influenced modern evolutionary and developmental biology.

[16] His investigation of the movement of water into and out of living egg cells (all the while maintaining their full developmental potential) gave insights into internal cellular structure that is now being more fully elucidated using powerful biophysical tools and computational methods.

[6] At the outbreak of World War II, Just was working at the Station Biologique in Roscoff, researching the paper that would become Unsolved Problems of General Biology.

[25] Beginning in 2000, the Medical University of South Carolina has hosted the annual Ernest E. Just Symposium to encourage non-white students to pursue careers in biomedical sciences and health professions.

[26] In 2008, a National Science Foundation-funded symposium honoring Just and his scientific work was held on the campus of Howard University, where he was a faculty member from 1907 until his death in 1941.

In 2013, an international symposium honoring Just was held at the Stazione Zoologica Anton Dohrn in Naples, Italy, where Just had worked starting in 1929.

[33] A children's book about Just, titled The Vast Wonder of the World: Biologist Ernest Everett Just, written by Mélina Mangal and illustrated by Luisa Uribe, was published by Millbrook Press in November 2018.

Living substance is such because it possesses this organization--something more than the sum of its minutest parts"[35] He argued forcefully that the "ectoplasm," the outer region of the cytoplasm, and not the nucleus, constitutes the heart of the dynamic cell.