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The processes of collecting, integrating, and representing heterogeneous urban data in Urban Digital Twins (UDTs) pose significant challenges. Besides, the lack of initiators’ knowledge and experience may lead to severe consequences in the implementation, utilization, and maintenance of UDTs. This research identifies the challenges of UDT development in Tallinn, Estonia, and discusses the City of Tallinn’s approaches as a case study. By analyzing the literature, the technical challenges related to the integration of heterogeneous qualitative and quantitative data for creating and updating UDTs (e.g., data collection, modeling, data integration, storage, and maintenance) have been identified, classified, and discussed with relevant officials of the City of Tallinn. Outsourcing data collection, using open-source software, and cloud computing were alternative solutions applied in Tallinn to overcome the challenges. The research concludes that initiators should clarify their objectives, expectations, and resources before developing UDTs to efficiently allocate and manage their technological and human resources to mitigate potential future obstacles.