Information and communications technology and technology-enhanced learning have unquestionably transformed traditional teaching–learning processes and are positioned as key factors to promote quality education, one of the basic sustainable development goals of the 2030 agenda. Document annotation, which was traditionally carried out with pencil and paper and currently benefits from digital document annotation tools, is a representative example of this transformation. Using document annotation tools, students can enrich the documents with annotations that highlight the most relevant aspects of these documents. As the conceptual complexity of the learning domain increases, the annotation of the documents may require comprehensive domain knowledge and an expert analysis capability that students usually lack. Consequently, a proliferation of irrelevant, incorrect, and/or poorly decontextualized annotations may appear, while other relevant aspects are completely ignored by the students. The main hypothesis proposed by this paper is that the use of a guiding annotation ontology in the annotation activities is a keystone aspect to alleviate these shortcomings. Consequently, comprehension is improved, exhaustive content analysis is promoted, and meta-reflective thinking is developed. To test this hypothesis, we describe our own annotation tool, @note, which fully implements this ontology-enhanced annotation paradigm, and we provide experimental evidence about how @note can improve academic performance via a pilot study concerning critical literary annotation.