Indoor navigation systems incorporating augmented reality allow users to locate places within buildings and acquire more knowledge about their environment. However, although diverse works have been introduced with varied technologies, infrastructure, and functionalities, a standardization of the procedures for elaborating these systems has not been reached. Moreover, while systems usually handle contextual information of places in proprietary formats, a platform-independent model is desirable, which would encourage its access, updating, and management. This paper proposes a methodology for developing indoor navigation systems based on the integration of Augmented Reality and Semantic Web technologies to present navigation instructions and contextual information about the environment. It comprises four modules to define a spatial model, data management (supported by an ontology), positioning and navigation, and content visualization. A mobile application system was developed for testing the proposal in academic environments, modeling the structure, routes, and places of two buildings from independent institutions. The experiments cover distinct navigation tasks by participants in both scenarios, recording data such as navigation time, position tracking, system functionality, feedback (answering a survey), and a navigation comparison when the system is not used. The results demonstrate the system’s feasibility, where the participants show a positive interest in its functionalities.