Upon returning to Lisbon at the age of 34, M. Farinha dos Santos enrolled in the remaining courses needed to complete his degree and attended a free archaeology course taught by Manuel Afonso do Paço (1895-1968). Under the guidance of Manuel Heleno (1894-1970), his professor at FLUL and director of the Museu Etnológico Português Dr. Leite de Vasconcelos [Dr. Leite de Vasconcelos Portuguese Ethnological Museum] (MEPLV), M. Farinha dos Santos studied the terra sigillata specimens in the museum’s collections as part of his work on his final dissertation, titled “Contribuição para um melhor conhecimento de terra sigillata encontrada em Portugal. A terra sigillata do Museu Etnológico do Dr. Leite de Vasconcelos” [Contribution to a better knowledge of terra sigillata found in Portugal. Dr. Leite de Vasconcelos Portuguese Ethnological Museum's terra sigillata].

Between 1957 and 1963, M. Farinha dos Santos participated in the Troia excavations alongside M. Heleno, taking on the role of director in 1960. In 1958, he became an "occasional contributor" of the MEPLV and joined the executive committee of the First National Archaeological Congress. Graduating with Lower Second-Class Honours (2.2), M. Farinha dos Santos was invited by M. Heleno in 1959 to become a "second assistant" in the History Section at FLUL. Consequently, he requested to be discharged from PIDE the following year. He subsequently taught annual courses in Prehistory, History of Roman Civilisation, and History of Art in Portugal, as well as semester courses in Oriental Antiquity and Numismatics, while also leading practical classes at the MEPLV, affiliated with FLUL.

M. Farinha dos Santos also studied speleology at the Portuguese Speleological Society (1948) under the guidance of Carl Harpsoe, then the Danish consul in Portugal, and geologist Jaime Martins Ferreira (1927-2011). He assisted José Camarate França (1923-1963) and others in discovering prehistoric sites in the municipalities of Sintra and Loures. He also completed the course for Conservators of Museums, Palaces, and National Monuments, graduating in first place with First-Class Honours. As a result, he was appointed professor of that course and director of the National Pantheon in 1968. However, he was removed from this position in 1975 (and later reinstated in 1982) under Decree-Law 123/75 of 11 March, which mandated the dismissal of all former PIDE officials from civil service (A História da PIDE, 2007).

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