This paper describes concepts, design, implementation, and performance evaluation of a 3D-based user interface for accessing IoT-based Smart Environments (IoT-SE). The generic interaction model of the described work addresses some major challenges of Human-IoT-SE-Interaction such as cognitive overload associated with manual device selection in complex IoT-SE, loss of user control, missing system image or over-automation. To address these challenges we propose a 3D-based mobile interface for mixed-initiative interaction in IoT-SE. The 3D visualization and 3D UI, acting as the central feature of the system, create a logical link between physical devices and their virtual representation on the end user's mobile devices. By so doing, the user can easily identify a device within the environment based on its position, orientation, and form, and access the identified devices through the 3D interface for direct manipulation within the scene. This overcomes the problem of manual device selection. In addition, the 3D visualization provides a system image for the IoT-SE, which supports users in understanding the ambience and things going on in it. Furthermore, the mobile interface allows users to control the amount and the way the IoT-SE automates the environment. For example, users can stop or postpone system triggered automatic actions, if they don't like or want them. Users also can remove a rule forever. By so doing, users can delete smart behaviors of their IoT-SE. This helps to overcome the automation challenges. In this paper, we present the design, implementation and evaluation of the proposed interaction system. We chose smart meeting rooms as the context for prototyping and evaluating our interaction concepts. However, the presented concepts and methods are generic and could be adapted to similar environments such as smart homes. We conducted a subjective usability evaluation (ISO-Norm 9241/110) with 16 users. All in one the study results indicate that the proposed 3D-User Interface achieved a good high score according to the ISO-Norm scores.