Presence is widely recognized as a key quality metric for immersive virtual reality (IVR) experiences. However, research on factors contributing to presence is impeded by the plethora of identified factors, contradictory results, and unclear interactions. Based on the analysis of the current literature, we propose a two-step research methodology combining exploratory and confirmatory paradigms to address these issues. As existing IVR study tools do not focus on presence and its determinants, we developed our own tool consisting of two components: an IVR app, based on Unreal Engine for designing and displaying IVR scenarios, and a browser-based experimenter interface using Vue.js, enabling precise control over presence factors and study procedure. The methodology and study tool underwent a formative expert evaluation (N = 6) and a first practical application within the AgeVR research project (N = 115). Their feasibility was confirmed by expert feedback, as well as data from 115 successfully completed exploratory studies with participants of various ages. The exploratory study procedure works for general presence, involvement, and plausibility illusion. Measures that will enable the seamless investigation of the remaining presence subcomponents are proposed. Our next step is to develop and test hypotheses in the confirmatory studies. The study tool was made publicly available as an open source project.