In 1986 he published Temas de Antropologia em Oliveira Martins, where he developed his historical analysis, with a strong anthropological inclination, through a grounded critique of the 'systematic evolutionism' of Oliveira Martins. Viegas Guerreiro counterposed the need for recognition of the multiplicity of processes of cultural development (not necessarily continuously progressive) and the importance of individual behaviour as an engine of change to the linearity of that evolutionary perspective. Completely rejecting the use of the concept of 'race', he condemned the way 'scientific progress of European cultures brought about, naturally, a deep conviction of superiority, a rambling ethnocentrism, which came to fruition in the most heinous forms of racism' (Temas de Antropologia em Oliveira Martins, 1986, 51), defending the autonomy of the concepts of race, culture, religion and morals, and, above all, detaching them from any kind of causal or deterministic relationship. He advocated the study of culture purged of any kind of value judgment, understood as an addiction of European ethnocentrism. .

In 1988 he finished editing Etnografia Portuguesa (‘Portuguese Ethnography’, started in 1933), publishing the 10th volume of the work, and in the same year, along with Agostinho da Silva, he created the 'Association of General Non-Degree Studies'. Looking to promote free public education, Viegas Guerreiro took over the Association and actively participated throughout the following years in the activities it promoted, resulting in multiple conferences in cooperation with various local authorities and universities.

In 1993, following his work on the 'Collection and Study of Folk Literature', he was responsible for founding the Centre for Portuguese Folk Traditions. In the Azores in 1995, at the age of eighty-three, he produced his final last research paper, entitled A Ilha de São Jorge: uma monografia (São Jorge Island: a monograph). On 1 May 1997, following a stroke that had left him unable to work, he died at Carnaxide Hospital.

He was a corresponding member of the Brazilian Association of Folklore (since 1967), corresponding associate of the Academy of Sciences of Lisbon (elected in 1976) and later Full Scholar of the Arts and Literature of the same Academy (in 1989). Currently, of the various institutions that inherited Viegas Guerreiro's research, three stand out for explicitly honouring his thinking and his name: the Professor Manuel Viegas Guerreiro Centre for Portuguese Folk Traditions, a research unit of the Faculty of Arts and Literarture at the University of Lisbon, the Manuel Viegas Guerreiro Centre for African Studies, a research center in the same Faculty, and finally, the Manuel Viegas Guerreiro Foundation, created in 2000 and whose headquarters is located in the birthplace of its namesake, Querença.

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