Although virtual reality became popular technology whose application is recognized in various domains, the field generally still lacks a widespread culture of usability. This is also evident when considering environments intended for learning, specifically virtual learning environments (VLEs). According to our findings, it is clear that there is a growing need for systematic evaluation approach to help with the design and development of usable learner-centered VLE solutions. After comprehensive introductory background and state of the art in the field, this article provides an insight into Scenario-based Group Usability Testing (ScerGUT), a mixed methods approach to the evaluation of three-dimensional VLEs which integrates several different methods of usability testing with measurements of educational value. While the majority of the existing work has made use of usually one single usability assessment technique, ScerGUT employs a number of methods putting in focus users and user testing. To examine efficiency and applicability of the approach, empirical validation is conducted as a case study of particular VLE. The contribution of the article is twofold: (a) ScerGUT as a mixed methods approach to the evaluation of VLEs, which brings new scientific value and could help other researchers and (b) ScerGUT's application to a particular VLE, which brings quantitative and qualitative results, thus providing an insight into ease of use and educational value of specific VLE.