He truly inaugurated his historiographical work, however, five years earlier, when he was 35 years old, with the publication of 1809: o Pôrto sob a segunda invasão francesa (1809: Porto Under the Second French Invasion), which earned him some public recognition as a researcher and scholar in the field of History. Echoes in the press praised the monograph and its author for its extensive documentary research, much of it previously unpublished from the manuscript holdings of the Public Library and Historical Archive of the Municipality of Porto, as well as its intelligent historical scholarship and rigorous scientific impartiality in piecing together the Napoleonic invasions and their effects on the city and the northern region during the second military campaign. In fact, in 1930, his reputation as a researcher was established with two new milestones: the study Alguns documentos inéditos sobre Uriel da Costa (Some unpublished documents about Uriel da Costa) announced new biographical facts about the famous Porto Jewish-convert philosopher, and in the pages of the newspaper O Primeiro de Janeiro he started the weekly series Falam velhos manuscritos..., (Old manuscripts say…) which he continued until the end of his life, amassing a total of around 1500 historical, cultural and artistic articles about Porto and various aspects of Portuguese history.

The closure of First Faculty of Arts in the summer of 1931 brought a halt to Magalhães Basto's university teaching career, forcing him to work as a secondary school teacher in the city's private schools. His dedication to new themes of historical research, and increasingly centred on Porto, however, grew with his designation as chief registrar and notary of the Santa Casa da Misericórdia do Porto (House of Mercy) registry office (1933) and as head of the department of manuscripts and reserves at the Porto Municipal Public Library (1934-1938).

In this last position, preparing the Catálogo do Fundo Azevedo (Catalog of Fundo Azevedo) and Catálogo dos Manuscritos Ultramarinos (Catalog of Overseas Manuscripts) offered him access to and knowledge of a rich collection of documentation on national and local history, including many previously unpublished medieval chronicles, which constitute much of the support for his future historiographical work. In 1934, he published the História da Santa Casa da Misericórdia do Porto, a case study of the local House of Mercy institution, which established his qualities as historian and showed some influences on the maturation of his thought and scientific model.

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