We present a workflow for seamless real-time navigation and 3D thermal mapping in combined indoor and outdoor environments in a global reference frame. The automated workflow and partly real-time capabilities are of special interest for inspection tasks and also for other time-critical applications. We use a hand-held integrated positioning system (IPS), which is a real-time capable visual-aided inertial navigation technology, and augment it with an additional passive thermal infrared camera and global referencing capabilities. The global reference is realized through surveyed optical markers (AprilTags). Due to the sensor data’s fusion of the stereo camera and the thermal images, the resulting georeferenced 3D point cloud is enriched with thermal intensity values. A challenging calibration approach is used to geometrically calibrate and pixel-co-register the trifocal camera system. By fusing the terrestrial dataset with additional geographic information from an unmanned aerial vehicle, we gain a complete building hull point cloud and automatically reconstruct a semantic 3D model. A single-family house with surroundings in the village of Morschenich near the city of Jülich (German federal state North Rhine-Westphalia) was used as a test site to demonstrate our workflow. The presented work is a step towards automated building information modeling.