Data recordings of the movement of vehicles can be enriched with heterogeneous and multimodal data beyond latitude, longitude, and timestamp and enhanced with complementary segmentations, constituting a semantic trajectory. Semantic Web (SW) technologies have been extensively used for the semantic integration of heterogeneous and multimodal movement-related data, and for the effective modeling of semantic trajectories, in several domains. In this paper, we present an integrated solution for the engineering of cultural heritage semantic trajectories generated from unmanned aerial vehicles (UAVs) and represented as knowledge graphs (KGs). Particularly, this work is motivated by, and evaluated based on, the application domain of UAV missions for documenting regions/points of cultural heritage interest. In this context, this research work extends our previous work on UAV semantic trajectories, contributing (a) an updated methodology for the engineering of semantic trajectories as KGs (STaKG), (b) an implemented toolset for the management of KG-based semantic trajectories, (c) a refined ontology for the representation of knowledge related to UAV semantic trajectories and to cultural heritage documentation, and (d) the application and evaluation of the proposed methodology, the developed toolset, and the ontology within the domain of UAV-based cultural heritage documentation. The evaluation of the integrated UAV solution was achieved by exploiting real datasets collected during three UAV missions to document sites of cultural interest in Lesvos, Greece, i.e., the UNESCO-protected petrified forest of Lesvos Petrified Forest/Geopark, the village of Vrissa, and University Hill.