Dissatisfied with the traditional text-dominated approach to Egyptology of the time, Baumgartel decided to focus on archaeology in her doctoral studies at the University of Königsberg.
This challenged the prevailing hyper-diffusionist views of Grafton Elliot Smith, who argued that almost all elements of human culture originated in Egypt and spread outwards.
During this time she participated in excavations, including at Wadi Sheik in Egypt and Monte Gargano in Italy, and visited ancient and modern flint mines across Europe.
The archaeological and Egyptological communities in England rallied to obtain monetary support for her work: Sir John L. Myres arranged a grant for her to compile a bibliography of prehistoric Italy and Malta, and she also taught evening classes on the Egyptian language for University College London (UCL).
Glanville therefore enthusiastically accepted Baumgartel's offer, and arranged for her work to be supported by the Petrie collection's patron Sir Robert Mond, and later by the department itself.
In particular, she challenged her teacher Kurt Sethe's thesis that Egyptian civilization originated in the Nile Delta, instead stressing, based on archaeological evidence, the primacy of Upper Egypt.
When a number of Petrie's notebooks were found in a box under a telephone at UCL, Baumgartel prepared them for publication along with her now extensive catalogue of Naqada artefacts in collections.
However, by now her work was being heavily criticised for its reliance on now outdated diffusionist ideas, as well as her staunch insistence that Lower Egypt was a "cultural backwater" in the predynastic period, despite mounting evidence to the contrary in the form of new discoveries and the new technique of radiocarbon dating.