Formal Ontology in Information Systems (FOIS) is the flagship conference of the International Association for Ontology and its Applications, a non-profit organization promoting interdisciplinary research and international collaboration at the intersection of philosophical ontology, linguistics, logic, cognitive science, and computer science. This book presents the 11 papers accepted for the 12th edition of FOIS. The conference was held from 13-17 September 2021 in Bozen-Bolzano, Italy, as a hybrid event with some participants attending on-site in Bolzano and others attending virtually online. The papers are divided into 3 sections and cover a wide range of topics: (1) Foundations, addressing fundamental issues; (2) Applications and Methods, presenting novel uses, systems, tools, and approaches; and (3) Domain Ontology, describing well-formed ontologies in particular subject areas.