Over the past decade, virtual museums have rapidly evolved due to technological advancements, and after the COVID-19 disruption grew in importance, this sustained the innovation of storytelling and the digital transformation of touristic practices. This paper presents the outcomes of a cooperation project: a virtual museum for eight ports in the Adriatic area, constituting notable examples of widespread heritage. The platform Adrijo is a multi-scalar, multilayer virtual museum that leverages the concept of geo-storytelling and e-tourism, also applying two augmented reality technologies for site-specific installations. In addition to the project results, an assessment of the different levels and experiences is provided, based on qualitative and qualitative analysis. As a re-usable resource, the technical tender specification from the methodological work package is presented, encompassing details of the technology, structure, functionalities, costs, timing for realization, and accessibility for disabled people. This paper proposes, through the critical analysis of the VM, a methodology that can be reused in other contexts, also providing toolkits for both its implementation and user satisfaction surveys, as well as for analyzing the strengths and weaknesses of some specific examples. The goal of the present research is thus to establish a consolidated methodological framework for designing, developing, implementing, and assessing a virtual museum, fully featured with 3D models and augmented reality technologies.