His academic career began in 1961 at the University of Porto, first, as a monitor (assistente extraordinário) and, later, as an assistant lecturer. In 1964 he was sent on a commission to Angola to join the academic staff of the newly founded University of Luanda, then named Angola General University Studies. In 1966, after being appointed assistant lecturer of this university, he was sent to the University of Exeter with a scholarship to take further studies aimed at a Ph.D. on Organic Chemistry. In 1970 he was appointed visiting lecturer of the Department of Chemistry of this university and took post doctoral studies for two further years still under a scholarship of the Portuguese government. Back to Angola in 1971, he became in charge of the Department of Chemistry of the Faculty of Science of the University of Luanda, as assistant professor.
On returning to Portugal, in 1975 he was appointed assistant professor and, in 1980, professor of Chemistry at the University of Minho, where he founded the Department of Chemistry and, later, the Institute of Biotechnology and Fine Chemistry, to which he presided until 1995 and 1996, respectively.
He was one of the founding members of the European Peptide Society and the first elected president of the Organic Chemistry Division of the Portuguese Society of Chemistry. He was the chairman of several scientific meetings in Portugal and also of the 23rd European Peptide Symposium and was a member of the scientific committees of the 22nd-25th editions of this symposium (Interlaken, Braga, Edinburgh and Budapest, 1992-1998).
He was a member of the Grants Committee of the Portuguese Foundation for Science and Technology (FCT) and also of the first External Evaluation Committee appointed by the Portuguese Universities Foundation for evaluation of the Chemistry and Chemical Engineering courses and also of that for evaluation of the Chemical Education courses.

Peptide science with emphasis on synthesis of amino acids and peptides by conventional and unconventional methods, including electrochemical approaches. Patents litigation in the field of Organic Chemistry, mostly in connection with the drug and pharmaceutical industry.

Organic Chemistry and Peptide Chemistry; as a subsidiary topic, also Cosmogony both in the School of Science of the University of Minho and in the Department of Applied Mathematics of the University of Porto (since 1980 and 1998, respectively). On this topic he has delivered several intensive courses in connection with the Ministries of Education of Portugal and Spain and also some sixty invited seminars in most Portuguese universities and in many polytechnic institutes and secondary schools and also in various cultural institutions. He founded and directed until 2006 in the University of Minho a master course (M.Sc.) on Evolution and Origin of Life.

• H.L.S. Maia, K.G. Orrell, B. Ridge, and H.N. Rydon, ‘Evaluation of the Equilibrium and Activation Parameters for the Interconversion of the Conformational Isomers of Some N-Acylprolines by Nuclear Magnetic Resonance Spectroscopy', J. Chem. Soc., Perkin Trans. II, 1976, 76125
• H.L.S. Maia, L. Monteiro, F. Degerbeck, L. Grehn e U. Ragnarsson, ‘Selective Cathodic Cleavage of Unsymmetrical Imidodicarbonates, Acylcarbamates and Diacylamides', J. Chem. Soc., Perkin Trans.II, 1993, 495
• P.M.T. Ferreira, H.L.S. Maia and L.S. Monteiro, ‘Efficient synthesis of dehydroamino acid derivatives’, Tetrahedron Lett., 39, 1998, 9575
• Filipa C.S.C. Pinto, Sílvia M.M.A. Pereira-Lima and Hernâni L.S. Maia, “Straightforward, racemization-free synthesis of peptides with fairly to very bulky di- and trisubstituted glycines”, Tetrahedron, 65, 2009, 9165–9179

• Hernâni L.S. Maia and J.J. Moura Ramos (eds.), A Evolução Cósmica e a Origem da Vida, Almedina, Coimbra, 1984 (science popularization)
• Hernâni L.S. Maia (ed.), Peptides 1994, Escom, Leiden, 1995 (conference proceedings)
• A.C. Fernandes, B. Herold, H. Maia. A.P. Rauter and J.A.R. Rodrigues, Guia IUPAC para a Nomenclatura de Compostos Orgânicos, Lidel, Lisbon, 2002 (translation)
• Ilda Dias and Hernâni L.S. Maia, Origem da Vida: Recentes Contribuições para um Modelo Científico, Escolar Editora, Lisbon, 2008 (science popularization)