In the mid 1930s, his career as a professor and scientist lost some of its momentum to politics. As a supporter of the Estado Novo, he was invited to serve as president of the Administrative Commission of the Municipality of Porto and agent in the Corporative Chamber (1936-1942), and deputy in the National Assembly for three terms (1945-1956). During his time on the Porto city council he encouraged cultural activities with the creation of the City Historian's Office (1936), the Portuguese Studies short course (1938) and the restoration of the National Museum of Soares dos Reis (1940). In 1942, at the invitation of the Ministry of the Colonies, he began working on the colonial reform project, focusing his attention on the fields of education and scientific research. For the interest and concern shown by his development, Mendes Corrêa was appointed to the presidency of the Geographical Missions and Colonial Research Committee (1946) and the Overseas Board of Governors (1958).

The question of the colonies became one of the leading and most original themes of his anthropological work, resulting from the research missions that took him to the Portugal's African territories, where he collected empirical knowledge that led him to resume, also in 1946, his university career. He assumed the direction of the Escola Superior Colonial (later the Instituto Superior de Estudos Ultramarinos) until his retirement from public office in 1958. His strong nationalist leanings toward "Portuguese imperialism" featured prominently in his new role, firmly rooting the school's educational mission to train workers with knowledge of local contexts. The ultimate goal of these highly educated civil servants would be to respond to the governmental concerns of the Salazar regime, strengthening Portuguese nationalism in the colonies and cooperating with Portuguese scientists for scientific research.

Mendes Corrêa's extensive research in various areas of the Natural and Social Sciences ensured his name circulated among international intellectuals, with over three hundred publications and citations in the works of Raymond Furon, Afrânio Peixoto and Henri Breuil. This was equally proof of his constant contact with and updating on developments of the scientific world. Specifically in the field of history, he demonstrated himself to be one of the main drivers of prehistoric archaeology, reviewing previously published research and exploring new archaeological sites, suggesting a specificity and originality of the Iberian megalithic culture in the European context, and even suggesting a native species through the example of “Concheiros de Muge”, which he named Homo afer taganus.

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