He has published over 60 papers in peer-reviewed international journals and given over 80 presentations at international conferences. For his academic work in developing particleboards from bio-waste, he was awarded the 'Postdoctoral Fellowship of Academic Excellence' by the Foundation of Greek Scholarships.

In 2015, in collaboration with Robert Heimann, he developed the innovative method of turbulent pyrolysis, producing biochar and biopetroleum from agricultural waste and biomass using only friction and without the addition of external heat.

Another notable aspect of his research was developing the 3T energy efficiency method for comprehensively assessing Waste-to-Energy units. He was a member of the Consultation Committee for the development of the GrEcoislands initiative, and he serves as a proposal evaluator for the Greek General Secretariat for Research and Technology and a reviewer for over 20 international academic journals.

Since 2018, Dr. Vakalis has been a member of the Global Council for Research and Technology of Energy Waste in collaboration with the Earth Engineering Center at Columbia University in New York. Mr. Vakalis is involved in the project to produce and analyze biochar to be applied in olive groves.