An open question in research nowadays is the usability of brain–computer interfaces (BCI) conceived to extend human capabilities of interaction within a virtual environment. Several paradigms are used for BCI, but the steady-state visual-evoked potential (SSVEP) stands out as it provides a higher information transfer rate while requiring less training. It is an electroencephalographic response detectable when the user looks at a flickering visual stimulus. This research proposes a novel approach for SSVEP-based BCI controller used here for navigation within a 3D virtual environment. For the first time, the flickering stimuli were integrated into virtual objects as a part of the virtual scene in a more transparent and ecological way. As an example, when navigating inside a virtual natural outdoor scene, we could embed the SSVEP flashes in the wings of virtual butterflies surrounding the user. We could also introduce the use of animated and moving stimulations when using SSVEP-based BCI, as the virtual butterflies were left with the possibility of moving and flying in front of the user. Moreover, users received real-time feedback of their mental activity and were thus aware of their detected SSVEP directly and continuously. An experiment has been conducted to assess the influence of both the feedback and the integrated controller on navigation performance and subjective preference. We found that the usage of a controller integrated within the virtual scene along with the feedback seems to improve subjective preference and feeling of presence, despite reduced performance in terms of speed. This suggests that SSVEP-based BCI interfaces for virtual environments could move on from static targets and use integrated and animated stimuli presented in an ecological way for controls in systems where performance demands could be relaxed to benefit an improvement in interaction naturalness.