His primary research focus is on biodiversity, particularly tropical lichens, encompassing systematics, floristic surveys, and taxonomic reviews.

He is a visiting professor at the Federal University of Mato Grosso do Sul in Campo Grande, Brazil, since February 2019.

In 2020, Aptroot was listed among the 100,000 most influential scientists in the world according to research published by Stanford University, which utilised citations from the Scopus database.

[5] Because of Aptroot's broad expertise in tropical lichens, his colleague Ingvar Kärnefelt has called him "a Müller Argoviensis of our time".

[3] Aptroot is the author or co-author of three of the thirty most highly cited publications published in the scientific journal The Lichenologist from 2000 to 2019.